Check the over-representation of functional terms
Si Liu, Wei Sun
2024-10-17
The code for 2024_09_UCSF_Bulk_EB_Timecourse dataset is in a separate file.
This code file can be applied to all other datasets from 2023_12 release to 2024_09 release.
In each setting, based on the processed output file, take all genes with non-NA adjusted pvalues as genes to consider, and significant genes based on adjusted p-value cutoff 0.05 and absolute log2foldchange cutoff log2(1.5).
R libraries.
library(ggplot2)
library(ggrepel)
library(ggpubr)
library(stringr)
library(RColorBrewer)
library(goseq)
library(fgsea)
library(dplyr)
library(data.table)
theme_set(theme_classic())
# BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene", force=TRUE)
# BiocManager::install("org.Hs.eg.db")
release_name = params$release_name
release_name## [1] "2023_12_JAX_RNAseq_ExtraEmbryonic"Prepare gene set information
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "gene_annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "gene_annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"sapply(pathways, length)## reactome go_bp
## 1692 7647Filter gene sets for size between 10 and 500.
lapply(pathways, function(v){
quantile(sapply(v, length), probs = seq(0, 1, 0.1), na.rm = TRUE)
})## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0for(k1 in names(pathways)){
p1 = pathways[[k1]]
pathways[[k1]] = p1[sapply(p1, length) %in% 10:500]
}
sapply(pathways, length)## reactome go_bp
## 1326 5320Read in gene annotation
gene_info = fread("data/gencode_v44_primary_assembly_info.tsv",
data.table = FALSE)
dim(gene_info)## [1] 62754 8gene_info[1:2,]## geneId chr strand start end ensembl_gene_id
## 1 ENSG00000000003.16 chrX - 100627108 100639991 ENSG00000000003
## 2 ENSG00000000005.6 chrX + 100584936 100599885 ENSG00000000005
## hgnc_symbol description
## 1 TSPAN6 tetraspanin 6 [Source:HGNC Symbol;Acc:HGNC:11858]
## 2 TNMD tenomodulin [Source:HGNC Symbol;Acc:HGNC:17757]Prepare for reading in DE results
result_dir = file.path("results", release_name)
processed_output_dir = file.path(result_dir, "processed")
all_result_files = list.files(path=processed_output_dir, pattern=".tsv",
all.files=TRUE, full.names=FALSE)
all_result_files = sort(all_result_files)
# condition_DE_files is for datasets with hypoxia and normoxia condition comparison
regular_DE_files = all_result_files[!grepl("hyp_vs_nor", all_result_files)]
condition_DE_files = all_result_files[grepl("hyp_vs_nor", all_result_files)]
# extract core strings from regular DE result files
extract_cores <- function(x, str_before, str_after){
pattern <- paste0(".*", str_before, "(.*?)", str_after, ".*")
middle_string <- sub(pattern, "\\1", x)
middle_substrings <- strsplit(middle_string, "_")[[1]]
x_d_group <- paste(middle_substrings[1:(length(middle_substrings)-1)],
collapse = "_")
x_gene <- middle_substrings[length(middle_substrings)]
return(c(x_d_group, x_gene))
}
df_file_info = NULL
for (x in regular_DE_files){
df_file_info = rbind(df_file_info,
extract_cores(x,
paste0(release_name, "_"),
"_DEseq2.tsv"))
}
df_file_info = as.data.frame(df_file_info)
colnames(df_file_info) = c("DE_general_group", "gene")
df_file_info$items = paste(df_file_info$DE_general_group,
df_file_info$gene, sep="_")
df_file_info$items## [1] "ExM_day_6_nor_ISL1" "PrS_day_6_hyp_EPAS1" "PrS_day_6_nor_EPAS1"
## [4] "PrS_day_6_nor_FOSB" "PrS_day_6_nor_GCM1" "PrS_day_6_nor_GRHL1"
## [7] "PrS_day_6_nor_POU2F3" "PrS_day_6_nor_PPARG"df_file_info## DE_general_group gene items
## 1 ExM_day_6_nor ISL1 ExM_day_6_nor_ISL1
## 2 PrS_day_6_hyp EPAS1 PrS_day_6_hyp_EPAS1
## 3 PrS_day_6_nor EPAS1 PrS_day_6_nor_EPAS1
## 4 PrS_day_6_nor FOSB PrS_day_6_nor_FOSB
## 5 PrS_day_6_nor GCM1 PrS_day_6_nor_GCM1
## 6 PrS_day_6_nor GRHL1 PrS_day_6_nor_GRHL1
## 7 PrS_day_6_nor POU2F3 PrS_day_6_nor_POU2F3
## 8 PrS_day_6_nor PPARG PrS_day_6_nor_PPARG# extract core strings from DE result files about hypoxia and normoxia conditions
extract_cores_cond <- function(x, str_before, str_after){
pattern <- paste0(".*", str_before, "(.*?)", str_after, ".*")
middle_string <- sub(pattern, "\\1", x)
middle_substrings <- strsplit(middle_string, "_")[[1]]
x_d_group <- paste(middle_substrings[1:(length(middle_substrings)-3)],
collapse = "_")
x_compare <- paste(middle_substrings[(length(middle_substrings)-2):length(middle_substrings)],
collapse = "_")
return(c(x_d_group, x_compare))
}
if (length(condition_DE_files)>0){
df_file_info_cond = NULL
for (x in condition_DE_files){
df_file_info_cond = rbind(df_file_info_cond,
extract_cores_cond(x,
paste0(release_name, "_"),
"_DEseq2.tsv"))
}
df_file_info_cond = as.data.frame(df_file_info_cond)
colnames(df_file_info_cond) = c("DE_general_group", "comparison")
df_file_info_cond$items = paste(df_file_info_cond$DE_general_group,
df_file_info_cond$comparison, sep="_")
print(df_file_info_cond$items)
print(df_file_info_cond)
}## [1] "PrS_day_6_EPAS1_CE_hyp_vs_nor" "PrS_day_6_EPAS1_KO_hyp_vs_nor"
## [3] "PrS_day_6_EPAS1_PTC_hyp_vs_nor" "PrS_day_6_WT_WT_hyp_vs_nor"
## DE_general_group comparison items
## 1 PrS_day_6_EPAS1_CE hyp_vs_nor PrS_day_6_EPAS1_CE_hyp_vs_nor
## 2 PrS_day_6_EPAS1_KO hyp_vs_nor PrS_day_6_EPAS1_KO_hyp_vs_nor
## 3 PrS_day_6_EPAS1_PTC hyp_vs_nor PrS_day_6_EPAS1_PTC_hyp_vs_nor
## 4 PrS_day_6_WT_WT hyp_vs_nor PrS_day_6_WT_WT_hyp_vs_nor# set an exception for UCSF dataRead in DE results and conduct enrichment analysis
Regular DE results
fc0 = log2(1.5)
p0 = 0.05
max_n2kp = 10
goseq_res = NULL
ko_start_col_index = 7
for (i in 1:nrow(df_file_info)){
it1 = df_file_info$items[i]
gene_name = df_file_info$gene[i]
res = fread(paste0("results/", release_name, "/processed/", release_name,
"_", it1, "_DEseq2.tsv"),
data.table = FALSE)
res[1:2,]
de_info_columns = colnames(res)[ko_start_col_index:ncol(res)]
strategy_vec = sapply(de_info_columns, function(x)strsplit(x, "_")[[1]][2])
unique_strategies = unique(strategy_vec)
for (ko1 in unique_strategies){
print(paste0(it1, " ", ko1))
de_gene_sets = list()
res_k = res[,c(1, grep(ko1, names(res)))]
names(res_k) = gsub(paste0(gene_name, "_", ko1, "_"), "", names(res_k))
res_k = res_k[!is.na(res_k$padj),]
ww_up = which((res_k$log2FoldChange > fc0) & (res_k$padj < p0))
ww_down = which((res_k$log2FoldChange < ((-1)*fc0)) & (res_k$padj < p0))
de_gene_sets[[paste0(ko1, "_up")]] = res_k[ww_up,]$gene_ID
de_gene_sets[[paste0(ko1, "_down")]] = res_k[ww_down,]$gene_ID
print(sapply(de_gene_sets, length))
print(table(res_k$gene_ID %in% gene_info$ensembl_gene_id))
gene_info_k = gene_info[gene_info$ensembl_gene_id %in% res_k$gene_ID,]
dim(gene_info_k)
gene_info_k[1:2,]
sum(is.na(gene_info_k$hgnc_symbol))
t_symbol = table(gene_info_k$hgnc_symbol)
table(t_symbol)
t_symbol[t_symbol > 1]
gene_info_k = gene_info_k[gene_info_k$hgnc_symbol %in% names(t_symbol)[t_symbol==1],]
dim(gene_info_k)
for(j in 1:length(de_gene_sets)){
if(length(de_gene_sets[[j]]) < 10) { next }
print(j)
set_j = names(de_gene_sets)[j]
genes = gene_info_k$ensembl_gene_id %in% de_gene_sets[[j]]
names(genes) = gene_info_k$hgnc_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=120)
set_j_fullname = paste0(it1, "_", set_j)
goseq_res[[set_j_fullname]][[k1]] = res1
}
}
}
}
}## [1] "ExM_day_6_nor_ISL1 CE"
## CE_up CE_down
## 340 312
##
## TRUE
## 16874
## [1] 1
## [1] 2
## [1] "ExM_day_6_nor_ISL1 KO"
## KO_up KO_down
## 165 240
##
## TRUE
## 15502
## [1] 1
## [1] 2
## [1] "ExM_day_6_nor_ISL1 PTC"
## PTC_up PTC_down
## 181 251
##
## TRUE
## 16422
## [1] 1
## [1] 2
## [1] "PrS_day_6_hyp_EPAS1 CE"
## CE_up CE_down
## 2266 1930
##
## TRUE
## 18336
## [1] 1
## [1] 2
## [1] "PrS_day_6_hyp_EPAS1 KO"
## KO_up KO_down
## 1306 834
##
## TRUE
## 17892
## [1] 1
## [1] 2
## [1] "PrS_day_6_hyp_EPAS1 PTC"
## PTC_up PTC_down
## 1547 1006
##
## TRUE
## 17893
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_EPAS1 CE"
## CE_up CE_down
## 769 603
##
## TRUE
## 16172
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_EPAS1 KO"
## KO_up KO_down
## 18 22
##
## TRUE
## 11649
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_EPAS1 PTC"
## PTC_up PTC_down
## 143 161
##
## TRUE
## 14825
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_FOSB CE"
## CE_up CE_down
## 361 48
##
## TRUE
## 16627
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_FOSB KO"
## KO_up KO_down
## 591 256
##
## TRUE
## 17502
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_FOSB PTC"
## PTC_up PTC_down
## 87 34
##
## TRUE
## 16628
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_GCM1 CE"
## CE_up CE_down
## 2263 3036
##
## TRUE
## 18923
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_GCM1 KO"
## KO_up KO_down
## 1782 2704
##
## TRUE
## 18929
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_GCM1 PTC"
## PTC_up PTC_down
## 1656 2599
##
## TRUE
## 18979
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_GRHL1 CE"
## CE_up CE_down
## 1384 2055
##
## TRUE
## 18937
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_GRHL1 KO"
## KO_up KO_down
## 1034 1449
##
## TRUE
## 18874
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_GRHL1 PTC"
## PTC_up PTC_down
## 2355 2740
##
## TRUE
## 18989
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_POU2F3 CE"
## CE_up CE_down
## 940 1098
##
## TRUE
## 17488
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_POU2F3 KO"
## KO_up KO_down
## 365 225
##
## TRUE
## 14825
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_POU2F3 PTC"
## PTC_up PTC_down
## 2 4
##
## TRUE
## 18988
## [1] "PrS_day_6_nor_PPARG CE"
## CE_up CE_down
## 2207 2296
##
## TRUE
## 19064
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_PPARG KO"
## KO_up KO_down
## 1395 1634
##
## TRUE
## 18880
## [1] 1
## [1] 2
## [1] "PrS_day_6_nor_PPARG PTC"
## PTC_up PTC_down
## 1672 2342
##
## TRUE
## 19033
## [1] 1
## [1] 2
### DE results about hypoxia vs normoxia conditions if available
## Keep using the same
## goseq_res
## object
if (length(condition_DE_files)>0){
fc0 = log2(1.5)
p0 = 0.05
max_n2kp = 10
ko_start_col_index = 7
for (i in 1:nrow(df_file_info_cond)){
it1 = df_file_info_cond$items[i]
compare_name = df_file_info_cond$comparison[i]
print(compare_name)
res = fread(paste0("results/", release_name, "/processed/", release_name,
"_", it1, "_DEseq2.tsv"),
data.table = FALSE)
res[1:2,]
de_info_columns = colnames(res)[ko_start_col_index:ncol(res)]
de_gene_sets = list()
res_k = res[,c(1, grep(compare_name, names(res)))]
names(res_k) = gsub(paste0(compare_name, "_"), "", names(res_k))
res_k = res_k[!is.na(res_k$padj),]
ww_up = which((res_k$log2FoldChange > fc0) & (res_k$padj < p0))
ww_down = which((res_k$log2FoldChange < ((-1)*fc0)) & (res_k$padj < p0))
de_gene_sets[[paste0("up")]] = res_k[ww_up,]$gene_ID
de_gene_sets[[paste0("down")]] = res_k[ww_down,]$gene_ID
print(sapply(de_gene_sets, length))
print(table(res_k$gene_ID %in% gene_info$ensembl_gene_id))
gene_info_k = gene_info[gene_info$ensembl_gene_id %in% res_k$gene_ID,]
dim(gene_info_k)
gene_info_k[1:2,]
sum(is.na(gene_info_k$hgnc_symbol))
t_symbol = table(gene_info_k$hgnc_symbol)
table(t_symbol)
t_symbol[t_symbol > 1]
gene_info_k = gene_info_k[gene_info_k$hgnc_symbol %in% names(t_symbol)[t_symbol==1],]
dim(gene_info_k)
for(j in 1:length(de_gene_sets)){
if(length(de_gene_sets[[j]]) < 10) { next }
print(j)
set_j = names(de_gene_sets)[j]
genes = gene_info_k$ensembl_gene_id %in% de_gene_sets[[j]]
names(genes) = gene_info_k$hgnc_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=120)
set_j_fullname = paste0(it1, "_", set_j)
goseq_res[[set_j_fullname]][[k1]] = res1
}
}
}
}
}## [1] "hyp_vs_nor"
## up down
## 1894 1624
##
## TRUE
## 15660
## [1] 1
## [1] 2
## [1] "hyp_vs_nor"
## up down
## 1216 1302
##
## TRUE
## 15018
## [1] 1
## [1] 2
## [1] "hyp_vs_nor"
## up down
## 1855 1809
##
## TRUE
## 16546
## [1] 1
## [1] 2
## [1] "hyp_vs_nor"
## up down
## 3324 3400
##
## TRUE
## 19162
## [1] 1
## [1] 2
Save results out
names(goseq_res)## [1] "ExM_day_6_nor_ISL1_CE_up" "ExM_day_6_nor_ISL1_CE_down"
## [3] "ExM_day_6_nor_ISL1_KO_up" "ExM_day_6_nor_ISL1_KO_down"
## [5] "ExM_day_6_nor_ISL1_PTC_up" "ExM_day_6_nor_ISL1_PTC_down"
## [7] "PrS_day_6_hyp_EPAS1_CE_up" "PrS_day_6_hyp_EPAS1_CE_down"
## [9] "PrS_day_6_hyp_EPAS1_KO_up" "PrS_day_6_hyp_EPAS1_KO_down"
## [11] "PrS_day_6_hyp_EPAS1_PTC_up" "PrS_day_6_hyp_EPAS1_PTC_down"
## [13] "PrS_day_6_nor_EPAS1_CE_up" "PrS_day_6_nor_EPAS1_CE_down"
## [15] "PrS_day_6_nor_EPAS1_PTC_up" "PrS_day_6_nor_FOSB_CE_up"
## [17] "PrS_day_6_nor_FOSB_KO_up" "PrS_day_6_nor_FOSB_PTC_up"
## [19] "PrS_day_6_nor_GCM1_CE_up" "PrS_day_6_nor_GCM1_CE_down"
## [21] "PrS_day_6_nor_GCM1_KO_up" "PrS_day_6_nor_GCM1_KO_down"
## [23] "PrS_day_6_nor_GCM1_PTC_up" "PrS_day_6_nor_GCM1_PTC_down"
## [25] "PrS_day_6_nor_GRHL1_CE_up" "PrS_day_6_nor_GRHL1_CE_down"
## [27] "PrS_day_6_nor_GRHL1_KO_up" "PrS_day_6_nor_GRHL1_KO_down"
## [29] "PrS_day_6_nor_GRHL1_PTC_up" "PrS_day_6_nor_GRHL1_PTC_down"
## [31] "PrS_day_6_nor_POU2F3_CE_up" "PrS_day_6_nor_POU2F3_CE_down"
## [33] "PrS_day_6_nor_POU2F3_KO_up" "PrS_day_6_nor_PPARG_CE_up"
## [35] "PrS_day_6_nor_PPARG_CE_down" "PrS_day_6_nor_PPARG_KO_up"
## [37] "PrS_day_6_nor_PPARG_KO_down" "PrS_day_6_nor_PPARG_PTC_up"
## [39] "PrS_day_6_nor_PPARG_PTC_down" "PrS_day_6_EPAS1_CE_hyp_vs_nor_up"
## [41] "PrS_day_6_EPAS1_CE_hyp_vs_nor_down" "PrS_day_6_EPAS1_KO_hyp_vs_nor_up"
## [43] "PrS_day_6_EPAS1_KO_hyp_vs_nor_down" "PrS_day_6_EPAS1_PTC_hyp_vs_nor_up"
## [45] "PrS_day_6_EPAS1_PTC_hyp_vs_nor_down" "PrS_day_6_WT_WT_hyp_vs_nor_up"
## [47] "PrS_day_6_WT_WT_hyp_vs_nor_down"for(n1 in names(goseq_res)){
print(n1)
print(goseq_res[[n1]])
}## [1] "ExM_day_6_nor_ISL1_CE_up"
## $reactome
## category over_represented_pvalue
## 525 interferon gamma signaling 2.796105e-06
## 384 formation of the cornified envelope 4.223776e-06
## 572 keratinization 5.143913e-06
## 524 interferon alpha beta signaling 1.151508e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 525 0.9999996 11 73 0.002271895
## 384 0.9999996 8 37 0.002271895
## 572 0.9999996 8 38 0.002271895
## 524 0.9999838 8 58 0.038143700
##
## $go_bp
## category over_represented_pvalue
## 1502 leukocyte migration 3.124554e-06
## 2914 positive regulation of defense response 7.945702e-06
## 4728 response to type ii interferon 9.460662e-06
## 717 defense response to symbiont 1.112058e-05
## 555 cellular response to type ii interferon 1.142714e-05
## 39 acute inflammatory response 1.264366e-05
## 4523 regulation of vasculature development 1.769723e-05
## 2789 positive regulation of acute inflammatory response 2.019111e-05
## 1893 myeloid leukocyte migration 2.306438e-05
## 1824 mononuclear cell migration 2.489424e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1502 0.9999992 19 242 0.01120439
## 2914 0.9999977 22 336 0.01120439
## 4728 0.9999985 11 94 0.01120439
## 717 0.9999971 18 241 0.01120439
## 555 0.9999984 10 78 0.01120439
## 39 0.9999985 9 63 0.01120439
## 4523 0.9999955 17 225 0.01323627
## 2789 0.9999992 5 16 0.01323627
## 1893 0.9999953 13 143 0.01323627
## 1824 0.9999953 12 122 0.01323627
##
## [1] "ExM_day_6_nor_ISL1_CE_down"
## $reactome
## category
## 345 extracellular matrix organization
## 306 ecm proteoglycans
## 608 met activates ptk2 signaling
## 252 degradation of the extracellular matrix
## 428 germ layer formation at gastrulation
## 183 collagen chain trimerization
## 611 met promotes cell motility
## 84 assembly of collagen fibrils and other multimeric structures
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 345 4.300776e-09 1.0000000 23 234
## 306 5.939069e-06 0.9999994 9 59
## 608 3.428814e-05 0.9999976 6 28
## 252 5.036838e-05 0.9999907 11 108
## 428 8.027500e-05 0.9999973 4 12
## 183 1.777108e-04 0.9999823 6 37
## 611 2.203652e-04 0.9999770 6 39
## 84 2.284038e-04 0.9999699 7 51
## FDR
## 345 5.698528e-06
## 306 3.934633e-03
## 608 1.514393e-02
## 252 1.668453e-02
## 428 2.127288e-02
## 183 3.782939e-02
## 611 3.782939e-02
## 84 3.782939e-02
##
## $go_bp
## category over_represented_pvalue
## 876 embryonic skeletal system development 1.798390e-11
## 4552 renal system development 6.187987e-10
## 367 cardiocyte differentiation 4.307276e-09
## 371 cartilage development 4.908175e-09
## 5000 striated muscle tissue development 1.128264e-08
## 948 epithelial cell proliferation 1.725666e-08
## 165 appendage morphogenesis 2.166131e-08
## 877 embryonic skeletal system morphogenesis 2.818212e-08
## 3896 regulation of epithelial cell proliferation 3.020359e-08
## 1022 external encapsulating structure organization 5.393876e-08
## under_represented_pvalue numDEInCat numInCat FDR
## 876 1 17 91 9.562041e-08
## 4552 1 27 274 1.645076e-06
## 367 1 17 122 6.524191e-06
## 371 1 19 162 6.524191e-06
## 5000 1 21 201 1.199796e-05
## 948 1 28 352 1.529228e-05
## 165 1 16 122 1.645332e-05
## 877 1 12 66 1.784361e-05
## 3896 1 25 295 1.784361e-05
## 1022 1 23 261 2.867924e-05
##
## [1] "ExM_day_6_nor_ISL1_KO_up"
## $reactome
## category over_represented_pvalue
## 524 interferon alpha beta signaling 8.529484e-06
## 525 interferon gamma signaling 4.379451e-05
## 773 peptide hormone biosynthesis 5.067351e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 524 0.9999993 7 54 0.01130157
## 525 0.9999956 7 69 0.02238080
## 773 0.9999995 3 6 0.02238080
##
## $go_bp
## category over_represented_pvalue
## 2914 positive regulation of defense response 2.469644e-09
## 39 acute inflammatory response 2.504879e-07
## 4008 regulation of innate immune response 3.072348e-07
## 41 acute phase response 3.369740e-07
## 4679 response to molecule of bacterial origin 3.958030e-07
## 717 defense response to symbiont 4.643181e-07
## 4362 regulation of response to cytokine stimulus 4.798123e-07
## 3257 positive regulation of response to biotic stimulus 1.206691e-06
## 555 cellular response to type ii interferon 2.734116e-06
## 4734 response to virus 2.849596e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 2914 1.0000000 19 306 0.0000131311
## 39 1.0000000 8 56 0.0003644517
## 4008 0.9999999 16 294 0.0003644517
## 41 1.0000000 6 25 0.0003644517
## 4679 0.9999999 14 227 0.0003644517
## 717 0.9999999 14 230 0.0003644517
## 4362 0.9999999 11 135 0.0003644517
## 3257 0.9999998 14 249 0.0008019969
## 555 0.9999998 8 76 0.0015151303
## 4734 0.9999994 15 307 0.0015151303
##
## [1] "ExM_day_6_nor_ISL1_KO_down"
## $reactome
## category over_represented_pvalue
## 345 extracellular matrix organization 3.032496e-09
## 306 ecm proteoglycans 4.830913e-06
## 252 degradation of the extracellular matrix 1.872737e-05
## 673 ncam1 interactions 9.464331e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 345 1.0000000 20 226 4.018057e-06
## 306 0.9999996 8 56 3.200480e-03
## 252 0.9999972 10 103 8.271254e-03
## 673 0.9999940 5 28 3.135060e-02
##
## $go_bp
## category over_represented_pvalue
## 876 embryonic skeletal system development 7.574622e-13
## 4850 sensory system development 6.910581e-11
## 869 embryonic organ development 8.799471e-11
## 877 embryonic skeletal system morphogenesis 3.542110e-10
## 5000 striated muscle tissue development 7.906715e-10
## 367 cardiocyte differentiation 8.514814e-10
## 1877 muscle tissue development 9.403096e-10
## 371 cartilage development 3.662875e-09
## 165 appendage morphogenesis 4.066712e-09
## 335 cardiac cell development 5.731365e-09
## under_represented_pvalue numDEInCat numInCat FDR
## 876 1 16 80 4.027426e-09
## 4850 1 26 287 1.559560e-07
## 869 1 27 329 1.559560e-07
## 877 1 12 57 4.708350e-07
## 5000 1 20 195 7.142323e-07
## 367 1 16 119 7.142323e-07
## 1877 1 25 316 7.142323e-07
## 371 1 17 156 2.402523e-06
## 165 1 15 118 2.402523e-06
## 335 1 12 68 3.047367e-06
##
## [1] "ExM_day_6_nor_ISL1_PTC_up"
## $reactome
## category over_represented_pvalue
## 773 peptide hormone biosynthesis 3.806996e-05
## 525 interferon gamma signaling 6.881161e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 773 0.9999996 3 6 0.04558769
## 525 0.9999925 7 72 0.04558769
##
## $go_bp
## category over_represented_pvalue
## 2914 positive regulation of defense response 1.760132e-07
## 713 defense response to bacterium 9.279269e-07
## 4008 regulation of innate immune response 2.034887e-06
## 717 defense response to symbiont 2.596090e-06
## 3257 positive regulation of response to biotic stimulus 6.661021e-06
## 1390 interleukin 8 production 8.814822e-06
## 1502 leukocyte migration 1.294731e-05
## 4734 response to virus 1.427926e-05
## 4362 regulation of response to cytokine stimulus 1.587860e-05
## 3037 positive regulation of interleukin 8 production 2.323508e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2914 1.0000000 18 329 0.0009358623
## 713 0.9999999 11 132 0.0024668936
## 4008 0.9999996 16 309 0.0034508522
## 717 0.9999995 14 238 0.0034508522
## 3257 0.9999987 14 265 0.0070833295
## 1390 0.9999993 7 57 0.0078114012
## 1502 0.9999975 13 236 0.0093807245
## 4734 0.9999968 15 316 0.0093807245
## 4362 0.9999977 10 139 0.0093807245
## 3037 0.9999984 6 44 0.0123435999
##
## [1] "ExM_day_6_nor_ISL1_PTC_down"
## $reactome
## category over_represented_pvalue
## 345 extracellular matrix organization 1.569637e-09
## 306 ecm proteoglycans 9.044888e-06
## 252 degradation of the extracellular matrix 3.657581e-05
## 183 collagen chain trimerization 5.798062e-05
## 608 met activates ptk2 signaling 1.157039e-04
## 182 collagen biosynthesis and modifying enzymes 1.174285e-04
## 517 integrin cell surface interactions 1.290048e-04
## 673 ncam1 interactions 2.322916e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 345 1.0000000 21 230 2.079769e-06
## 306 0.9999991 8 58 5.992238e-03
## 252 0.9999941 10 106 1.615432e-02
## 183 0.9999953 6 37 1.920608e-02
## 608 0.9999924 5 27 2.441877e-02
## 182 0.9999860 7 60 2.441877e-02
## 517 0.9999844 7 63 2.441877e-02
## 673 0.9999819 5 31 3.847329e-02
##
## $go_bp
## category over_represented_pvalue
## 165 appendage morphogenesis 9.110328e-10
## 876 embryonic skeletal system development 1.267501e-09
## 335 cardiac cell development 8.269869e-09
## 5000 striated muscle tissue development 9.574313e-09
## 367 cardiocyte differentiation 1.373615e-08
## 164 appendage development 2.409646e-08
## 4552 renal system development 2.603281e-08
## 1022 external encapsulating structure organization 2.789701e-08
## 371 cartilage development 6.122406e-08
## 869 embryonic organ development 6.403277e-08
## under_represented_pvalue numDEInCat numInCat FDR
## 165 1 16 121 3.369650e-06
## 876 1 14 90 3.369650e-06
## 335 1 12 69 1.272666e-05
## 5000 1 19 199 1.272666e-05
## 367 1 15 122 1.460702e-05
## 164 1 16 152 1.854105e-05
## 4552 1 22 271 1.854105e-05
## 1022 1 21 259 1.854105e-05
## 371 1 16 161 3.404622e-05
## 869 1 24 347 3.404622e-05
##
## [1] "PrS_day_6_hyp_EPAS1_CE_up"
## $reactome
## category
## 1300 unfolded protein response upr
## 561 ire1alpha activates chaperones
## 55 amino acids regulate mtorc1
## 1120 signaling by vegf
## 1092 signaling by interleukins
## 512 insertion of tail anchored proteins into the endoplasmic reticulum membrane
## 155 cellular response to starvation
## 946 response of eif2ak1 hri to heme deficiency
## 1005 ros and rns production in phagocytes
## 950 response to metal ions
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1300 4.000875e-06 0.9999987 33 89
## 561 2.449957e-05 0.9999937 21 50
## 55 2.640615e-05 0.9999928 22 54
## 1120 4.249383e-05 0.9999840 33 98
## 1092 5.960855e-05 0.9999655 90 362
## 512 6.222716e-05 0.9999906 12 22
## 155 1.197661e-04 0.9999442 44 154
## 946 2.165991e-04 0.9999744 9 15
## 1005 2.351095e-04 0.9999514 13 28
## 950 2.428115e-04 0.9999827 7 10
## FDR
## 1300 0.005301159
## 561 0.011662714
## 55 0.011662714
## 1120 0.013741832
## 1092 0.013741832
## 512 0.013741832
## 155 0.022670007
## 946 0.028767309
## 1005 0.028767309
## 950 0.028767309
##
## $go_bp
## category
## 4612 response to endoplasmic reticulum stress
## 1425 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
## 3690 regulation of autophagy
## 961 er nucleus signaling pathway
## 4693 response to oxygen levels
## 1578 macroautophagy
## 4722 response to topologically incorrect protein
## 4078 regulation of macroautophagy
## 5308 wound healing
## 4364 regulation of response to endoplasmic reticulum stress
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4612 2.242089e-12 1.0000000 82 244
## 1425 3.677141e-08 1.0000000 27 58
## 3690 4.212716e-08 1.0000000 89 328
## 961 1.263554e-07 1.0000000 22 44
## 4693 5.486186e-07 1.0000000 77 286
## 1578 7.165219e-07 1.0000000 84 324
## 4722 1.041395e-06 0.9999996 47 149
## 4078 1.120731e-06 0.9999996 48 153
## 5308 1.666703e-06 0.9999994 85 330
## 4364 1.834866e-06 0.9999995 29 76
## FDR
## 4612 1.192118e-08
## 1425 7.466336e-05
## 3690 7.466336e-05
## 961 1.679580e-04
## 4693 5.834010e-04
## 1578 6.349578e-04
## 4722 7.448658e-04
## 4078 7.448658e-04
## 5308 9.457810e-04
## 4364 9.457810e-04
##
## [1] "PrS_day_6_hyp_EPAS1_CE_down"
## $go_bp
## category over_represented_pvalue
## 2642 pattern specification process 1.657623e-07
## 214 axon guidance 1.206103e-06
## 1681 mesenchymal cell migration 3.793624e-06
## 165 appendage morphogenesis 1.156013e-05
## 999 establishment of tissue polarity 2.314907e-05
## 337 cardiac chamber development 2.419292e-05
## 164 appendage development 2.812277e-05
## 3902 regulation of establishment of planar polarity 2.882584e-05
## 2417 neural crest cell differentiation 3.806520e-05
## 2166 negative regulation of locomotion 4.169198e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2642 1.0000000 59 335 0.0008813579
## 214 0.9999996 37 180 0.0032064259
## 1681 0.9999992 17 55 0.0067235658
## 165 0.9999964 25 116 0.0153662992
## 999 0.9999942 18 67 0.0191583720
## 337 0.9999913 29 140 0.0191583720
## 164 0.9999899 28 145 0.0191583720
## 3902 0.9999938 15 50 0.0191583720
## 2417 0.9999890 20 84 0.0221676277
## 2166 0.9999807 45 279 0.0221676277
##
## [1] "PrS_day_6_hyp_EPAS1_KO_up"
## $reactome
## category over_represented_pvalue
## 631 metallothioneins bind metals 2.645965e-06
## 950 response to metal ions 4.355962e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 631 1.0000000 6 7 0.002885825
## 950 0.9999998 7 10 0.002885825
##
## $go_bp
## category over_represented_pvalue
## 5308 wound healing 1.216152e-07
## 1417 intracellular zinc ion homeostasis 1.200437e-06
## 4540 regulation of wound healing 4.743033e-06
## 486 cellular response to copper ion 1.175619e-05
## 4612 response to endoplasmic reticulum stress 1.436308e-05
## 4372 regulation of response to wounding 1.531815e-05
## 1255 hemostasis 1.559951e-05
## 405 cell chemotaxis 1.725306e-05
## 1497 leukocyte chemotaxis 1.907057e-05
## 770 detoxification of copper ion 2.288500e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 5308 1.0000000 59 325 0.0006466282
## 1417 0.9999999 12 27 0.0031913622
## 4540 0.9999987 24 97 0.0084062363
## 486 0.9999989 9 19 0.0110996677
## 4612 0.9999938 43 244 0.0110996677
## 4372 0.9999947 28 130 0.0110996677
## 1255 0.9999941 33 166 0.0110996677
## 405 0.9999930 37 198 0.0110996677
## 1497 0.9999932 29 141 0.0110996677
## 770 0.9999991 6 9 0.0110996677
##
## [1] "PrS_day_6_hyp_EPAS1_KO_down"
## $reactome
## category over_represented_pvalue
## 183 collagen chain trimerization 2.838308e-05
## 252 degradation of the extracellular matrix 2.869374e-05
## 184 collagen degradation 7.509535e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 183 0.9999964 9 36 0.01900961
## 252 0.9999930 16 105 0.01900961
## 184 0.9999874 10 49 0.03316711
##
## $go_bp
## category over_represented_pvalue
## 214 axon guidance 2.431541e-10
## 337 cardiac chamber development 6.186260e-08
## 363 cardiac ventricle development 1.431092e-07
## 869 embryonic organ development 4.013514e-07
## 5000 striated muscle tissue development 4.494209e-07
## 1701 metanephric nephron development 4.692003e-07
## 339 cardiac chamber morphogenesis 6.795407e-07
## 1681 mesenchymal cell migration 9.218570e-07
## 2642 pattern specification process 1.895457e-06
## 367 cardiocyte differentiation 2.065181e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 214 1.0000000 31 175 1.292850e-06
## 337 1.0000000 24 138 1.644617e-04
## 363 1.0000000 20 103 2.536372e-04
## 869 0.9999999 40 351 4.157896e-04
## 5000 0.9999999 28 203 4.157896e-04
## 1701 1.0000000 10 29 4.157896e-04
## 339 0.9999999 19 104 5.161597e-04
## 1681 0.9999999 13 53 6.126892e-04
## 2642 0.9999993 37 334 1.010690e-03
## 367 0.9999995 20 125 1.010690e-03
##
## [1] "PrS_day_6_hyp_EPAS1_PTC_up"
## $go_bp
## category
## 4050 regulation of leukocyte proliferation
## 1997 negative regulation of cell adhesion
## 4005 regulation of inflammatory response
## 477 cellular response to biotic stimulus
## 1504 leukocyte proliferation
## 1996 negative regulation of cell activation
## 3657 regulation of alpha beta t cell activation
## 98 amino acid transmembrane transport
## 49 adenylate cyclase activating g protein coupled receptor signaling pathway
## 1322 immune response regulating cell surface receptor signaling pathway
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4050 8.316028e-06 0.9999968 36 168
## 1997 1.423492e-05 0.9999939 43 220
## 4005 1.673653e-05 0.9999925 48 258
## 477 3.233090e-05 0.9999869 35 169
## 1504 3.764762e-05 0.9999832 42 221
## 1996 4.109780e-05 0.9999842 31 144
## 3657 4.612576e-05 0.9999867 20 76
## 98 6.389899e-05 0.9999817 19 73
## 49 7.542630e-05 0.9999757 22 89
## 1322 7.570516e-05 0.9999657 40 215
## FDR
## 4050 0.02966271
## 1997 0.02966271
## 4005 0.02966271
## 477 0.03503581
## 1504 0.03503581
## 1996 0.03503581
## 3657 0.03503581
## 98 0.03551148
## 49 0.03551148
## 1322 0.03551148
##
## [1] "PrS_day_6_hyp_EPAS1_PTC_down"
## $reactome
## category
## 183 collagen chain trimerization
## 184 collagen degradation
## 252 degradation of the extracellular matrix
## 306 ecm proteoglycans
## 345 extracellular matrix organization
## 517 integrin cell surface interactions
## 182 collagen biosynthesis and modifying enzymes
## 185 collagen formation
## 84 assembly of collagen fibrils and other multimeric structures
## 525 interferon gamma signaling
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 183 2.376243e-09 1.0000000 15 36
## 184 6.767919e-09 1.0000000 17 49
## 252 1.359401e-08 1.0000000 25 105
## 306 5.069385e-07 0.9999999 16 59
## 345 1.602928e-06 0.9999994 35 230
## 517 1.623816e-06 0.9999997 16 65
## 182 3.700694e-06 0.9999993 15 59
## 185 3.435642e-05 0.9999916 16 77
## 84 9.196376e-05 0.9999813 12 50
## 525 2.312451e-04 0.9999389 14 76
## FDR
## 183 3.148522e-06
## 184 4.483746e-06
## 252 6.004020e-06
## 306 1.679234e-04
## 345 3.585928e-04
## 517 3.585928e-04
## 182 7.004885e-04
## 185 5.690282e-03
## 84 1.353911e-02
## 525 3.063997e-02
##
## $go_bp
## category over_represented_pvalue
## 4896 skeletal system morphogenesis 2.370129e-10
## 876 embryonic skeletal system development 6.346006e-10
## 1239 heart morphogenesis 7.959646e-10
## 2400 negative regulation of viral process 1.241386e-09
## 870 embryonic organ morphogenesis 5.307787e-09
## 337 cardiac chamber development 7.292674e-09
## 1687 mesenchyme development 7.652884e-09
## 214 axon guidance 8.844539e-09
## 339 cardiac chamber morphogenesis 1.550810e-08
## 363 cardiac ventricle development 1.579762e-08
## under_represented_pvalue numDEInCat numInCat FDR
## 4896 1 36 173 1.260197e-06
## 876 1 24 87 1.410715e-06
## 1239 1 40 211 1.410715e-06
## 2400 1 22 75 1.650112e-06
## 870 1 39 216 5.644301e-06
## 337 1 30 138 5.812912e-06
## 1687 1 43 257 5.812912e-06
## 214 1 34 175 5.878302e-06
## 339 1 25 104 8.399592e-06
## 363 1 25 103 8.399592e-06
##
## [1] "PrS_day_6_nor_EPAS1_CE_up"
## $go_bp
## category over_represented_pvalue
## 4888 skeletal muscle cell differentiation 2.320281e-07
## 221 b cell activation 1.222738e-06
## 360 cardiac septum development 1.340714e-06
## 2428 neuroepithelial cell differentiation 1.418615e-06
## 1504 leukocyte proliferation 1.959461e-06
## 488 cellular response to decreased oxygen levels 2.034921e-06
## 499 cellular response to fatty acid 2.175119e-06
## 1823 mononuclear cell differentiation 2.347164e-06
## 361 cardiac septum morphogenesis 2.588976e-06
## 4619 response to fatty acid 3.928866e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 4888 1.0000000 15 55 0.001233693
## 221 0.9999996 28 185 0.001529510
## 360 0.9999997 19 95 0.001529510
## 2428 0.9999999 10 27 0.001529510
## 1504 0.9999994 29 203 0.001529510
## 488 0.9999995 22 128 0.001529510
## 499 0.9999998 9 24 0.001529510
## 1823 0.9999991 39 318 0.001529510
## 361 0.9999995 15 64 0.001529510
## 4619 0.9999995 11 38 0.002088978
##
## [1] "PrS_day_6_nor_EPAS1_CE_down"
## $reactome
## category
## 13 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 280 dna methylation
## 163 chromatin modifications during the maternal to zygotic transition mzt
## 464 hdacs deacetylate histones
## 189 condensation of prophase chromosomes
## 463 hcmv late events
## 1123 sirt1 negatively regulates rrna expression
## 86 assembly of the orc complex at the origin of replication
## 461 hcmv early events
## 983 rmts methylate histone arginines
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 13 1.797855e-07 1.0000000 12 57
## 280 2.117408e-07 1.0000000 12 57
## 163 4.570043e-07 0.9999999 12 61
## 464 7.490313e-07 0.9999999 14 88
## 189 8.064858e-07 0.9999999 12 65
## 463 2.337074e-06 0.9999996 15 109
## 1123 2.659755e-06 0.9999997 11 60
## 86 3.359696e-06 0.9999996 11 61
## 461 3.672982e-06 0.9999992 16 124
## 983 3.714706e-06 0.9999994 12 72
## FDR
## 13 0.0001400665
## 280 0.0001400665
## 163 0.0002015389
## 464 0.0002133961
## 189 0.0002133961
## 463 0.0004914556
## 1123 0.0004914556
## 86 0.0004914556
## 461 0.0004914556
## 983 0.0004914556
##
## [1] "PrS_day_6_nor_EPAS1_PTC_up"
## $reactome
## category over_represented_pvalue
## 615 metabolism of carbohydrates 3.293848e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 615 0.9999943 11 235 0.0435776
##
## [1] "PrS_day_6_nor_FOSB_CE_up"
## $reactome
## category
## 515 integrin cell surface interactions
## 343 extracellular matrix organization
## 1142 striated muscle contraction
## 250 degradation of the extracellular matrix
## 182 collagen chain trimerization
## 183 collagen degradation
## 84 assembly of collagen fibrils and other multimeric structures
## 181 collagen biosynthesis and modifying enzymes
## 184 collagen formation
## 1160 syndecan interactions
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 515 5.440956e-09 1.0000000 13 62
## 343 2.703210e-08 1.0000000 23 221
## 1142 7.384844e-08 1.0000000 8 24
## 250 1.426951e-07 1.0000000 15 102
## 182 3.685600e-07 1.0000000 9 35
## 183 5.365875e-07 1.0000000 10 47
## 84 5.922329e-07 0.9999999 10 47
## 181 3.205380e-06 0.9999996 10 57
## 184 4.154909e-06 0.9999994 11 72
## 1160 5.022808e-06 0.9999997 7 26
## FDR
## 515 7.198385e-06
## 343 1.788173e-05
## 1142 3.256716e-05
## 250 4.719639e-05
## 182 9.752097e-05
## 183 1.119320e-04
## 84 1.119320e-04
## 181 5.300897e-04
## 184 6.107716e-04
## 1160 6.645175e-04
##
## $go_bp
## category over_represented_pvalue
## 1022 external encapsulating structure organization 1.310736e-12
## 645 collagen fibril organization 3.123706e-11
## 82 ameboidal type cell migration 6.640154e-11
## 5000 striated muscle tissue development 7.295320e-11
## 1239 heart morphogenesis 4.981123e-10
## 1687 mesenchyme development 6.648361e-10
## 4997 striated muscle cell differentiation 2.878148e-09
## 5112 tissue migration 3.005691e-09
## 1877 muscle tissue development 6.213371e-09
## 371 cartilage development 1.463888e-08
## under_represented_pvalue numDEInCat numInCat FDR
## 1022 1 31 237 6.969182e-09
## 645 1 15 54 8.304373e-08
## 82 1 36 366 9.697305e-08
## 5000 1 26 196 9.697305e-08
## 1239 1 26 207 5.296926e-07
## 1687 1 28 246 5.891556e-07
## 4997 1 26 232 1.997658e-06
## 5112 1 28 270 1.997658e-06
## 1877 1 31 331 3.670721e-06
## 371 1 20 155 7.783491e-06
##
## [1] "PrS_day_6_nor_FOSB_KO_up"
## $reactome
## category
## 345 extracellular matrix organization
## 517 integrin cell surface interactions
## 306 ecm proteoglycans
## 252 degradation of the extracellular matrix
## 182 collagen biosynthesis and modifying enzymes
## 185 collagen formation
## 183 collagen chain trimerization
## 742 o glycosylation of tsr domain containing proteins
## 184 collagen degradation
## 84 assembly of collagen fibrils and other multimeric structures
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 345 2.231190e-13 1.0000000 39 234
## 517 1.344007e-10 1.0000000 18 66
## 306 3.842552e-09 1.0000000 16 61
## 252 1.421618e-08 1.0000000 21 109
## 182 2.939011e-08 1.0000000 15 59
## 185 2.618527e-07 1.0000000 16 77
## 183 4.622359e-07 1.0000000 11 37
## 742 8.256749e-07 0.9999999 11 36
## 184 1.732608e-06 0.9999998 12 50
## 84 3.645308e-06 0.9999995 12 52
## FDR
## 345 2.956326e-10
## 517 8.904049e-08
## 306 1.697127e-06
## 252 4.709109e-06
## 182 7.788378e-06
## 185 5.782580e-05
## 183 8.749464e-05
## 742 1.367524e-04
## 184 2.550785e-04
## 84 4.830033e-04
##
## $go_bp
## category over_represented_pvalue
## 82 ameboidal type cell migration 7.026619e-15
## 1022 external encapsulating structure organization 2.075346e-14
## 1877 muscle tissue development 2.842400e-14
## 5000 striated muscle tissue development 3.734463e-14
## 1239 heart morphogenesis 4.266013e-14
## 5112 tissue migration 5.314679e-14
## 645 collagen fibril organization 9.202014e-13
## 917 endothelial cell migration 1.360046e-12
## 1687 mesenchyme development 1.757070e-12
## 659 connective tissue development 8.410576e-12
## under_represented_pvalue numDEInCat numInCat FDR
## 82 1 54 379 3.736053e-11
## 1022 1 43 254 4.536478e-11
## 1877 1 50 339 4.536478e-11
## 5000 1 38 204 4.536478e-11
## 1239 1 39 211 4.536478e-11
## 5112 1 44 278 4.709691e-11
## 645 1 20 60 6.989587e-10
## 917 1 34 194 9.039206e-10
## 1687 1 40 252 1.038038e-09
## 659 1 36 224 4.471903e-09
##
## [1] "PrS_day_6_nor_FOSB_PTC_up"
## $reactome
## category over_represented_pvalue
## 343 extracellular matrix organization 1.017386e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 343 0.9999988 9 221 0.01346002
##
## [1] "PrS_day_6_nor_GCM1_CE_up"
## $reactome
## category
## 466 hdacs deacetylate histones
## 282 dna methylation
## 13 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 190 condensation of prophase chromosomes
## 1125 sirt1 negatively regulates rrna expression
## 606 meiotic recombination
## 827 prc2 methylates histones and dna
## 164 chromatin modifications during the maternal to zygotic transition mzt
## 86 assembly of the orc complex at the origin of replication
## 329 ercc6 csb and ehmt2 g9a positively regulate rrna expression
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 466 7.628865e-32 1 57 89
## 282 4.165369e-31 1 45 58
## 13 8.012020e-30 1 44 58
## 190 9.972113e-30 1 47 66
## 1125 1.421274e-29 1 45 61
## 606 1.889171e-29 1 51 77
## 827 3.455870e-28 1 46 66
## 164 5.346084e-28 1 45 64
## 86 1.037239e-27 1 44 62
## 329 6.504127e-26 1 45 69
## FDR
## 466 1.010825e-28
## 282 2.759557e-28
## 13 3.303262e-27
## 190 3.303262e-27
## 1125 3.766375e-27
## 606 4.171919e-27
## 827 6.541468e-26
## 164 8.854451e-26
## 86 1.527047e-25
## 329 8.617968e-24
##
## $go_bp
## category
## 2553 nucleosome organization
## 3484 protein localization to cenp a containing chromatin
## 3450 protein dna complex assembly
## 3487 protein localization to chromosome centromeric region
## 3485 protein localization to chromatin
## 2184 negative regulation of megakaryocyte differentiation
## 199 attachment of spindle microtubules to kinetochore
## 2592 organelle fission
## 4885 sister chromatid segregation
## 1793 mitotic sister chromatid segregation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2553 1.970103e-14 1.0000000 46 115
## 3484 8.990333e-14 1.0000000 16 18
## 3450 2.710481e-11 1.0000000 59 202
## 3487 4.493061e-11 1.0000000 22 40
## 3485 3.491510e-08 1.0000000 23 55
## 2184 6.315881e-08 1.0000000 12 18
## 199 6.775164e-08 1.0000000 21 49
## 2592 2.638740e-07 1.0000000 88 424
## 4885 6.866750e-07 0.9999998 54 224
## 1793 8.266640e-07 0.9999997 47 185
## FDR
## 2553 1.047504e-10
## 3484 2.390080e-10
## 3450 4.803876e-08
## 3487 5.972401e-08
## 3485 3.712872e-05
## 2184 5.146221e-05
## 199 5.146221e-05
## 2592 1.753773e-04
## 4885 4.056723e-04
## 1793 4.395373e-04
##
## [1] "PrS_day_6_nor_GCM1_CE_down"
## $reactome
## category
## 1300 unfolded protein response upr
## 1127 slc mediated transmembrane transport
## 1211 thyroxine biosynthesis
## 1276 transport of bile salts and organic acids metal ions and amine compounds
## 262 diseases associated with glycosaminoglycan metabolism
## 561 ire1alpha activates chaperones
## 1120 signaling by vegf
## 1308 vegfr2 mediated vascular permeability
## 797 pi3k akt signaling in cancer
## 773 peptide hormone biosynthesis
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1300 1.373377e-05 0.9999952 34 90
## 1127 1.465164e-05 0.9999931 59 185
## 1211 4.242209e-05 1.0000000 6 6
## 1276 4.311032e-05 0.9999868 25 60
## 262 6.120233e-05 0.9999865 17 34
## 561 9.265976e-05 0.9999734 21 50
## 1120 9.552444e-05 0.9999614 35 101
## 1308 9.586607e-05 0.9999818 14 27
## 797 1.223141e-04 0.9999549 29 79
## 773 1.614522e-04 0.9999914 7 9
## FDR
## 1300 0.009706711
## 1127 0.009706711
## 1211 0.014280293
## 1276 0.014280293
## 262 0.015877817
## 561 0.015877817
## 1120 0.015877817
## 1308 0.015877817
## 797 0.018007360
## 773 0.021392421
##
## $go_bp
## category
## 49 adenylate cyclase activating g protein coupled receptor signaling pathway
## 4540 regulation of wound healing
## 4873 signal release
## 4050 regulation of leukocyte proliferation
## 1867 muscle cell differentiation
## 5308 wound healing
## 5115 tolerance induction
## 4679 response to molecule of bacterial origin
## 254 biomineral tissue development
## 1333 import across plasma membrane
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 49 2.407926e-07 0.9999999 37 90
## 4540 8.111677e-07 0.9999997 39 101
## 4873 2.561781e-06 0.9999988 105 385
## 4050 2.616669e-06 0.9999989 57 178
## 1867 3.768912e-06 0.9999983 91 325
## 5308 4.138258e-06 0.9999979 94 339
## 5115 4.829115e-06 0.9999995 13 20
## 4679 5.436606e-06 0.9999974 73 250
## 254 6.463327e-06 0.9999974 46 136
## 1333 6.829057e-06 0.9999970 52 157
## FDR
## 49 0.001280294
## 4540 0.002156489
## 4873 0.003256707
## 4050 0.003256707
## 1867 0.003256707
## 5308 0.003256707
## 5115 0.003256707
## 4679 0.003256707
## 254 0.003256707
## 1333 0.003256707
##
## [1] "PrS_day_6_nor_GCM1_KO_up"
## $reactome
## category
## 13 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 282 dna methylation
## 190 condensation of prophase chromosomes
## 1125 sirt1 negatively regulates rrna expression
## 466 hdacs deacetylate histones
## 827 prc2 methylates histones and dna
## 86 assembly of the orc complex at the origin of replication
## 606 meiotic recombination
## 164 chromatin modifications during the maternal to zygotic transition mzt
## 757 oxidative stress induced senescence
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 13 2.074386e-31 1 43 58
## 282 2.785576e-31 1 43 58
## 190 2.931739e-30 1 45 66
## 1125 6.939695e-30 1 43 61
## 466 9.213743e-30 1 52 89
## 827 1.117953e-28 1 44 66
## 86 4.714334e-28 1 42 62
## 606 3.173461e-27 1 46 76
## 164 3.802281e-27 1 42 64
## 757 1.600800e-25 1 56 116
## FDR
## 13 1.845444e-28
## 282 1.845444e-28
## 190 1.294851e-27
## 1125 2.298774e-27
## 466 2.441642e-27
## 827 2.468813e-26
## 86 8.923562e-26
## 606 5.256045e-25
## 164 5.597802e-25
## 757 2.121060e-23
##
## $go_bp
## category
## 2553 nucleosome organization
## 3484 protein localization to cenp a containing chromatin
## 3487 protein localization to chromosome centromeric region
## 3450 protein dna complex assembly
## 2184 negative regulation of megakaryocyte differentiation
## 3485 protein localization to chromatin
## 2592 organelle fission
## 4090 regulation of megakaryocyte differentiation
## 3486 protein localization to chromosome
## 4161 regulation of myeloid cell differentiation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2553 1.979412e-17 1.0000000 46 115
## 3484 4.618459e-15 1.0000000 16 18
## 3487 1.151894e-12 1.0000000 22 40
## 3450 2.203885e-12 1.0000000 55 202
## 2184 7.868912e-09 1.0000000 12 18
## 3485 4.096094e-08 1.0000000 21 55
## 2592 2.629131e-07 1.0000000 77 423
## 4090 2.877743e-07 1.0000000 15 34
## 3486 8.745217e-07 0.9999997 30 114
## 4161 2.558540e-06 0.9999991 37 161
## FDR
## 2553 1.052453e-13
## 3484 1.227817e-11
## 3487 2.041540e-09
## 3450 2.929514e-09
## 2184 8.367801e-06
## 3485 3.629822e-05
## 2592 1.912620e-04
## 4090 1.912620e-04
## 3486 5.166480e-04
## 4161 1.360376e-03
##
## [1] "PrS_day_6_nor_GCM1_KO_down"
## $reactome
## category
## 1276 transport of bile salts and organic acids metal ions and amine compounds
## 345 extracellular matrix organization
## 773 peptide hormone biosynthesis
## 1324 zinc transporters
## 629 metal ion slc transporters
## 1127 slc mediated transmembrane transport
## 269 diseases of glycosylation
## 262 diseases associated with glycosaminoglycan metabolism
## 665 muscle contraction
## 92 attachment and entry
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1276 9.033249e-06 0.9999976 24 61
## 345 2.761870e-05 0.9999862 63 243
## 773 4.537917e-05 0.9999981 7 9
## 1324 4.851570e-05 0.9999957 9 14
## 629 4.872277e-05 0.9999927 12 23
## 1127 6.110895e-05 0.9999708 50 185
## 269 9.593785e-05 0.9999587 38 129
## 262 1.229663e-04 0.9999726 15 34
## 665 1.284997e-04 0.9999403 43 155
## 92 1.581947e-04 0.9999784 10 18
## FDR
## 1276 0.01196906
## 345 0.01291154
## 773 0.01291154
## 1324 0.01291154
## 629 0.01291154
## 1127 0.01349489
## 269 0.01815966
## 262 0.01891801
## 665 0.01891801
## 92 0.02096080
##
## $go_bp
## category over_represented_pvalue
## 4540 regulation of wound healing 4.121137e-07
## 4050 regulation of leukocyte proliferation 1.340747e-06
## 1333 import across plasma membrane 2.917310e-06
## 1900 myotube differentiation 3.820701e-06
## 4269 regulation of polysaccharide metabolic process 4.871069e-06
## 5308 wound healing 5.041807e-06
## 5076 taxis 6.077965e-06
## 1867 muscle cell differentiation 7.149419e-06
## 1502 leukocyte migration 8.383686e-06
## 1504 leukocyte proliferation 9.701875e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 4540 0.9999999 36 102 0.002191209
## 4050 0.9999995 51 176 0.003564376
## 1333 0.9999988 47 156 0.004467882
## 1900 0.9999987 33 98 0.004467882
## 4269 0.9999991 17 36 0.004467882
## 5308 0.9999977 82 338 0.004467882
## 5076 0.9999970 79 325 0.004616649
## 1867 0.9999965 79 324 0.004751683
## 1502 0.9999960 68 271 0.004952896
## 1504 0.9999956 60 232 0.005158487
##
## [1] "PrS_day_6_nor_GCM1_PTC_up"
## $reactome
## category
## 282 dna methylation
## 466 hdacs deacetylate histones
## 13 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 190 condensation of prophase chromosomes
## 827 prc2 methylates histones and dna
## 1125 sirt1 negatively regulates rrna expression
## 86 assembly of the orc complex at the origin of replication
## 164 chromatin modifications during the maternal to zygotic transition mzt
## 606 meiotic recombination
## 757 oxidative stress induced senescence
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 282 1.167401e-26 1 38 58
## 466 7.813261e-26 1 46 89
## 13 1.698567e-25 1 37 58
## 190 4.538252e-25 1 39 66
## 827 9.147834e-25 1 39 66
## 1125 2.293100e-24 1 37 61
## 86 6.179870e-24 1 37 62
## 164 3.066340e-23 1 37 64
## 606 1.649465e-22 1 40 77
## 757 2.146886e-22 1 50 117
## FDR
## 282 1.546806e-23
## 466 5.176285e-23
## 13 7.502005e-23
## 190 1.503296e-22
## 827 2.424176e-22
## 1125 5.063930e-22
## 86 1.169761e-21
## 164 5.078625e-21
## 606 2.428378e-20
## 757 2.844624e-20
##
## $go_bp
## category
## 3484 protein localization to cenp a containing chromatin
## 2553 nucleosome organization
## 3450 protein dna complex assembly
## 3487 protein localization to chromosome centromeric region
## 2184 negative regulation of megakaryocyte differentiation
## 3485 protein localization to chromatin
## 4090 regulation of megakaryocyte differentiation
## 4161 regulation of myeloid cell differentiation
## 2592 organelle fission
## 2213 negative regulation of myeloid cell differentiation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3484 6.242761e-16 1.0000000 16 18
## 2553 2.067844e-15 1.0000000 41 115
## 3450 1.240006e-11 1.0000000 50 202
## 3487 1.358815e-11 1.0000000 20 40
## 2184 1.935383e-09 1.0000000 12 18
## 3485 3.010988e-08 1.0000000 20 55
## 4090 6.273259e-08 1.0000000 15 34
## 4161 2.225727e-07 0.9999999 37 163
## 2592 4.715835e-06 0.9999978 68 426
## 2213 6.729962e-06 0.9999983 20 74
## FDR
## 3484 3.319276e-12
## 2553 5.497363e-12
## 3450 1.806204e-08
## 3487 1.806204e-08
## 2184 2.058086e-06
## 3485 2.668237e-05
## 4090 4.764989e-05
## 4161 1.479274e-04
## 2592 2.786011e-03
## 2213 3.578321e-03
##
## [1] "PrS_day_6_nor_GCM1_PTC_down"
## $reactome
## category
## 345 extracellular matrix organization
## 1276 transport of bile salts and organic acids metal ions and amine compounds
## 269 diseases of glycosylation
## 773 peptide hormone biosynthesis
## 1127 slc mediated transmembrane transport
## 665 muscle contraction
## 1300 unfolded protein response upr
## 774 peptide hormone metabolism
## 629 metal ion slc transporters
## 271 diseases of metabolism
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 345 2.538992e-05 0.9999874 63 240
## 1276 3.567279e-05 0.9999896 23 61
## 269 5.075084e-05 0.9999787 39 129
## 773 5.139355e-05 0.9999978 7 9
## 1127 9.085653e-05 0.9999558 50 186
## 665 1.263344e-04 0.9999409 44 158
## 1300 1.709589e-04 0.9999349 28 90
## 774 1.871275e-04 0.9999386 22 64
## 629 3.157434e-04 0.9999430 11 23
## 271 3.313700e-04 0.9998235 54 214
## FDR
## 345 0.01702411
## 1276 0.01702411
## 269 0.01702411
## 773 0.01702411
## 1127 0.02407698
## 665 0.02789886
## 1300 0.03099299
## 774 0.03099299
## 629 0.04390652
## 271 0.04390652
##
## $go_bp
## category
## 5308 wound healing
## 254 biomineral tissue development
## 4873 signal release
## 4540 regulation of wound healing
## 560 cellular response to vascular endothelial growth factor stimulus
## 4050 regulation of leukocyte proliferation
## 1333 import across plasma membrane
## 1299 hormone transport
## 1687 mesenchyme development
## 405 cell chemotaxis
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 5308 3.459466e-07 1.0000000 86 341
## 254 3.980891e-07 0.9999999 44 136
## 4873 4.399594e-07 1.0000000 94 384
## 4540 5.513155e-07 0.9999998 36 103
## 560 1.034616e-06 0.9999998 24 57
## 4050 2.115641e-06 0.9999991 51 178
## 1333 3.956322e-06 0.9999984 47 157
## 1299 4.151735e-06 0.9999983 64 246
## 1687 4.340907e-06 0.9999980 67 257
## 405 4.507151e-06 0.9999980 57 211
## FDR
## 5308 0.0007328362
## 254 0.0007328362
## 4873 0.0007328362
## 4540 0.0007328362
## 560 0.0011002107
## 4050 0.0018748107
## 1333 0.0023410892
## 1299 0.0023410892
## 1687 0.0023410892
## 405 0.0023410892
##
## [1] "PrS_day_6_nor_GRHL1_CE_up"
## $reactome
## category over_represented_pvalue
## 524 interferon alpha beta signaling 1.699588e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 524 1 19 62 0.0002251954
##
## $go_bp
## category over_represented_pvalue
## 4644 response to interferon beta 8.544205e-09
## 513 cellular response to interferon beta 3.839167e-08
## 1877 muscle tissue development 3.931756e-08
## 5000 striated muscle tissue development 6.105285e-08
## 1687 mesenchyme development 1.338063e-07
## 1239 heart morphogenesis 2.906312e-07
## 1680 mesenchymal cell differentiation 3.613632e-07
## 4901 smad protein signal transduction 1.320695e-06
## 4727 response to type i interferon 1.588718e-06
## 2642 pattern specification process 1.661192e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 4644 1.0000000 13 26 4.542954e-05
## 513 1.0000000 11 20 6.968382e-05
## 1877 1.0000000 59 346 6.968382e-05
## 5000 1.0000000 42 209 8.115451e-05
## 1687 1.0000000 47 257 1.422896e-04
## 1239 0.9999999 42 217 2.575477e-04
## 1680 0.9999999 41 215 2.744812e-04
## 4901 0.9999997 19 66 8.777666e-04
## 4727 0.9999997 19 68 8.832560e-04
## 2642 0.9999993 54 334 8.832560e-04
##
## [1] "PrS_day_6_nor_GRHL1_CE_down"
## $go_bp
## category
## 1299 hormone transport
## 477 cellular response to biotic stimulus
## 885 endocrine hormone secretion
## 887 endocrine process
## 2000 negative regulation of cell cell adhesion
## 49 adenylate cyclase activating g protein coupled receptor signaling pathway
## 1939 negative regulation of alpha beta t cell activation
## 1941 negative regulation of alpha beta t cell proliferation
## 4679 response to molecule of bacterial origin
## 3216 positive regulation of protein catabolic process
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1299 9.898823e-08 1.0000000 58 247
## 477 3.375355e-07 0.9999999 46 181
## 885 6.847593e-07 0.9999999 19 47
## 887 9.861500e-07 0.9999998 24 70
## 2000 1.036133e-06 0.9999996 38 143
## 49 1.410249e-06 0.9999996 28 91
## 1939 1.817206e-06 0.9999997 15 33
## 1941 4.266746e-06 0.9999998 8 11
## 4679 5.331365e-06 0.9999977 55 254
## 3216 5.703751e-06 0.9999976 45 195
## FDR
## 1299 0.0005263204
## 477 0.0008973382
## 885 0.0011018235
## 887 0.0011018235
## 2000 0.0011018235
## 49 0.0012497160
## 1939 0.0013802975
## 1941 0.0028357861
## 4679 0.0030326846
## 3216 0.0030326846
##
## [1] "PrS_day_6_nor_GRHL1_KO_up"
## $reactome
## category over_represented_pvalue
## 524 interferon alpha beta signaling 7.673542e-09
## 345 extracellular matrix organization 6.291363e-07
## 252 degradation of the extracellular matrix 5.661167e-06
## 306 ecm proteoglycans 8.504193e-06
## 525 interferon gamma signaling 1.720475e-05
## 183 collagen chain trimerization 3.180028e-05
## 517 integrin cell surface interactions 9.363410e-05
## 665 muscle contraction 9.469591e-05
## 182 collagen biosynthesis and modifying enzymes 1.469891e-04
## 184 collagen degradation 1.598360e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 524 1.0000000 19 62 1.016744e-05
## 345 0.9999998 38 243 4.168028e-04
## 252 0.9999984 22 112 2.500349e-03
## 306 0.9999983 15 62 2.817014e-03
## 525 0.9999961 16 77 4.559258e-03
## 183 0.9999949 11 38 7.022562e-03
## 517 0.9999776 14 68 1.568401e-02
## 665 0.9999654 25 158 1.568401e-02
## 182 0.9999657 13 60 2.117827e-02
## 184 0.9999652 12 52 2.117827e-02
##
## $go_bp
## category over_represented_pvalue
## 1877 muscle tissue development 1.741141e-09
## 5000 striated muscle tissue development 8.004665e-09
## 1451 kidney epithelium development 2.270402e-08
## 2397 negative regulation of viral genome replication 7.586162e-08
## 2409 nephron development 2.104257e-07
## 1687 mesenchyme development 1.028779e-06
## 2610 ossification 1.302951e-06
## 2400 negative regulation of viral process 1.309864e-06
## 4552 renal system development 1.626193e-06
## 1696 mesonephros development 1.786292e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 1877 1.0000000 54 345 9.257648e-06
## 5000 1.0000000 38 207 2.128040e-05
## 1451 1.0000000 27 122 4.023910e-05
## 2397 1.0000000 16 49 1.008391e-04
## 2409 0.9999999 26 127 2.237666e-04
## 1687 0.9999996 39 256 8.705681e-04
## 2610 0.9999995 48 348 8.705681e-04
## 2400 0.9999997 18 74 8.705681e-04
## 4552 0.9999994 41 274 9.471533e-04
## 1696 0.9999996 19 82 9.471533e-04
##
## [1] "PrS_day_6_nor_GRHL1_KO_down"
## $go_bp
## category over_represented_pvalue
## 3261 positive regulation of response to wounding 2.585208e-06
## 3372 positive regulation of wound healing 3.223483e-06
## 4679 response to molecule of bacterial origin 1.224157e-05
## 1299 hormone transport 1.356104e-05
## 4873 signal release 2.770920e-05
## 1295 hormone biosynthetic process 5.226929e-05
## 295 c21 steroid hormone biosynthetic process 6.297194e-05
## 477 cellular response to biotic stimulus 7.672578e-05
## 1298 hormone metabolic process 7.980428e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 3261 0.9999995 17 62 0.008569629
## 3372 0.9999994 15 50 0.008569629
## 4679 0.9999949 39 254 0.018026010
## 1299 0.9999944 38 247 0.018026010
## 4873 0.9999866 52 386 0.029465968
## 1295 0.9999892 13 51 0.046319300
## 295 0.9999946 7 16 0.047146593
## 477 0.9999698 29 181 0.047146593
## 1298 0.9999691 28 175 0.047146593
##
## [1] "PrS_day_6_nor_GRHL1_PTC_up"
## $reactome
## category over_represented_pvalue
## 517 integrin cell surface interactions 1.267443e-08
## 345 extracellular matrix organization 2.549363e-08
## 709 non integrin membrane ecm interactions 8.874315e-08
## 282 dna methylation 4.656990e-07
## 306 ecm proteoglycans 7.256488e-07
## 957 rho gtpase effectors 1.287106e-06
## 985 rmts methylate histone arginines 3.665050e-06
## 190 condensation of prophase chromosomes 4.636888e-06
## 183 collagen chain trimerization 4.682617e-06
## 252 degradation of the extracellular matrix 6.161534e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 517 1.0000000 28 68 1.679363e-05
## 345 1.0000000 65 243 1.688953e-05
## 709 1.0000000 24 56 3.919489e-05
## 282 0.9999999 22 58 1.542628e-04
## 306 0.9999998 24 62 1.922969e-04
## 957 0.9999996 67 298 2.842359e-04
## 985 0.9999990 24 73 6.893852e-04
## 190 0.9999988 22 66 6.893852e-04
## 183 0.9999991 17 38 6.893852e-04
## 252 0.9999978 34 112 7.476358e-04
##
## $go_bp
## category
## 82 ameboidal type cell migration
## 18 actin filament organization
## 38 actomyosin structure organization
## 4552 renal system development
## 2642 pattern specification process
## 1877 muscle tissue development
## 5112 tissue migration
## 1239 heart morphogenesis
## 398 cell cell adhesion via plasma membrane adhesion molecules
## 5308 wound healing
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 82 5.169906e-10 1 97 382
## 18 1.262618e-09 1 102 417
## 38 4.850766e-09 1 56 185
## 4552 1.007518e-08 1 74 273
## 2642 1.121394e-08 1 85 334
## 1877 2.570479e-08 1 85 343
## 5112 4.767414e-08 1 72 281
## 1239 5.525425e-08 1 61 218
## 398 7.978064e-08 1 64 219
## 5308 8.907983e-08 1 83 345
## FDR
## 82 2.748839e-06
## 18 3.356669e-06
## 38 8.597175e-06
## 4552 1.192490e-05
## 2642 1.192490e-05
## 1877 2.277873e-05
## 5112 3.621191e-05
## 1239 3.672336e-05
## 398 4.713263e-05
## 5308 4.736375e-05
##
## [1] "PrS_day_6_nor_GRHL1_PTC_down"
## $reactome
## category over_represented_pvalue
## 1300 unfolded protein response upr 1.276041e-06
## 90 atf6 atf6 alpha activates chaperone genes 1.347247e-05
## 79 asparagine n linked glycosylation 3.650391e-05
## 91 atf6 atf6 alpha activates chaperones 1.089538e-04
## 946 response of eif2ak1 hri to heme deficiency 1.306559e-04
## 561 ire1alpha activates chaperones 1.312578e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 1300 0.9999996 33 90 0.001690754
## 90 0.9999994 8 10 0.008925511
## 79 0.9999807 71 283 0.016122558
## 91 0.9999911 8 12 0.028986103
## 946 0.9999856 9 15 0.028986103
## 561 0.9999629 19 50 0.028986103
##
## $go_bp
## category
## 1299 hormone transport
## 4612 response to endoplasmic reticulum stress
## 887 endocrine process
## 3494 protein localization to endoplasmic reticulum
## 4679 response to molecule of bacterial origin
## 477 cellular response to biotic stimulus
## 1939 negative regulation of alpha beta t cell activation
## 885 endocrine hormone secretion
## 3657 regulation of alpha beta t cell activation
## 1941 negative regulation of alpha beta t cell proliferation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1299 2.888093e-08 1.0000000 72 249
## 4612 1.589375e-07 1.0000000 69 245
## 887 4.843992e-07 0.9999999 28 69
## 3494 1.268246e-06 0.9999997 27 68
## 4679 2.734772e-06 0.9999988 68 255
## 477 4.396961e-06 0.9999981 52 181
## 1939 4.776631e-06 0.9999991 17 35
## 885 5.917315e-06 0.9999987 20 46
## 3657 6.241900e-06 0.9999981 29 81
## 1941 7.518669e-06 0.9999996 9 12
## FDR
## 1299 0.0001535599
## 4612 0.0004225354
## 887 0.0008585168
## 3494 0.0016858155
## 4679 0.0029081562
## 477 0.0036281926
## 1939 0.0036281926
## 885 0.0036875758
## 3657 0.0036875758
## 1941 0.0039976765
##
## [1] "PrS_day_6_nor_POU2F3_CE_up"
## $reactome
## category over_represented_pvalue
## 517 integrin cell surface interactions 1.037525e-06
## 149 cell junction organization 6.662492e-06
## 144 cell cell communication 9.679569e-06
## 40 adherens junctions interactions 2.153966e-05
## 145 cell cell junction organization 2.232466e-05
## 466 hdacs deacetylate histones 4.919255e-05
## 631 metallothioneins bind metals 7.636329e-05
## 345 extracellular matrix organization 9.947772e-05
## 463 hcmv early events 1.345601e-04
## 173 class b 2 secretin family receptors 1.558919e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 517 0.9999998 16 65 0.001374720
## 149 0.9999984 19 96 0.004275143
## 144 0.9999972 22 126 0.004275143
## 40 0.9999963 12 46 0.005916035
## 145 0.9999951 15 70 0.005916035
## 466 0.9999881 15 89 0.010863354
## 631 0.9999985 4 6 0.014454480
## 345 0.9999595 30 233 0.016475997
## 463 0.9999585 18 126 0.019810236
## 173 0.9999659 12 56 0.020619466
##
## $go_bp
## category over_represented_pvalue
## 5112 tissue migration 4.906286e-10
## 1687 mesenchyme development 5.442005e-10
## 82 ameboidal type cell migration 1.759847e-09
## 1680 mesenchymal cell differentiation 1.662299e-08
## 38 actomyosin structure organization 2.025864e-08
## 18 actin filament organization 1.163100e-07
## 954 epithelial to mesenchymal transition 1.582246e-07
## 4548 renal filtration 2.247731e-07
## 4970 sprouting angiogenesis 4.621466e-07
## 428 cell matrix adhesion 7.251283e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 5112 1.0000000 46 278 1.446757e-06
## 1687 1.0000000 44 252 1.446757e-06
## 82 1.0000000 55 379 3.119035e-06
## 1680 1.0000000 37 212 2.154303e-05
## 38 1.0000000 33 182 2.154303e-05
## 18 1.0000000 53 407 1.030701e-04
## 954 1.0000000 28 148 1.201829e-04
## 4548 1.0000000 10 21 1.493898e-04
## 4970 0.9999999 22 106 2.730259e-04
## 428 0.9999998 32 194 3.713563e-04
##
## [1] "PrS_day_6_nor_POU2F3_CE_down"
## $go_bp
## category
## 1900 myotube differentiation
## 418 cell fate commitment
## 3206 positive regulation of potassium ion transmembrane transport
## 498 cellular response to extracellular stimulus
## 4697 response to peptide hormone
## 4168 regulation of myotube differentiation
## 295 c21 steroid hormone biosynthetic process
## 560 cellular response to vascular endothelial growth factor stimulus
## 1295 hormone biosynthetic process
## 3735 regulation of carbohydrate metabolic process
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1900 4.319177e-06 0.9999989 20 98
## 418 7.666638e-06 0.9999974 29 182
## 3206 1.918990e-05 0.9999983 8 20
## 498 3.175180e-05 0.9999870 34 247
## 4697 3.306172e-05 0.9999849 43 343
## 4168 3.329037e-05 0.9999952 10 33
## 295 3.395144e-05 0.9999974 7 16
## 560 4.253434e-05 0.9999913 13 55
## 1295 4.645070e-05 0.9999912 12 48
## 3735 4.881880e-05 0.9999832 24 151
## FDR
## 1900 0.02038176
## 418 0.02038176
## 3206 0.02135903
## 498 0.02135903
## 4697 0.02135903
## 4168 0.02135903
## 295 0.02135903
## 560 0.02135903
## 1295 0.02135903
## 3735 0.02135903
##
## [1] "PrS_day_6_nor_POU2F3_KO_up"
## $reactome
## category
## 464 hdacs deacetylate histones
## 461 hcmv early events
## 463 hcmv late events
## 983 rmts methylate histone arginines
## 825 prc2 methylates histones and dna
## 462 hcmv infection
## 280 dna methylation
## 13 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 1123 sirt1 negatively regulates rrna expression
## 271 diseases of programmed cell death
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 464 1.356736e-08 1.0000000 13 88
## 461 1.181835e-06 0.9999998 13 124
## 463 1.321121e-06 0.9999998 12 109
## 983 1.487783e-06 0.9999998 10 72
## 825 5.011437e-06 0.9999995 9 65
## 462 7.928422e-06 0.9999986 13 147
## 280 1.218431e-05 0.9999988 8 56
## 13 1.268151e-05 0.9999987 8 57
## 1123 1.765808e-05 0.9999981 8 60
## 271 1.971687e-05 0.9999971 10 94
## FDR
## 464 1.794961e-05
## 461 4.920841e-04
## 463 4.920841e-04
## 983 4.920841e-04
## 825 1.326026e-03
## 462 1.748217e-03
## 280 2.097205e-03
## 13 2.097205e-03
## 1123 2.391517e-03
## 271 2.391517e-03
##
## $go_bp
## category
## 82 ameboidal type cell migration
## 4901 smad protein signal transduction
## 5112 tissue migration
## 1875 muscle organ morphogenesis
## 1687 mesenchyme development
## 403 cell cell signaling by wnt
## 398 cell cell adhesion via plasma membrane adhesion molecules
## 425 cell junction disassembly
## 1680 mesenchymal cell differentiation
## 4399 regulation of smad protein signal transduction
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 82 4.252388e-08 1.0000000 27 353
## 4901 7.673828e-07 0.9999999 10 58
## 5112 2.282230e-06 0.9999994 20 260
## 1875 6.725705e-06 0.9999993 9 56
## 1687 1.221280e-05 0.9999968 18 238
## 403 1.401595e-05 0.9999956 23 369
## 398 4.106912e-05 0.9999899 15 170
## 425 4.779874e-05 0.9999976 5 17
## 1680 6.849303e-05 0.9999823 15 200
## 4399 7.701841e-05 0.9999935 6 32
## FDR
## 82 0.0002260995
## 4901 0.0020400872
## 5112 0.0040448716
## 1875 0.0089401433
## 1687 0.0124204674
## 403 0.0124204674
## 398 0.0311949287
## 425 0.0317682382
## 1680 0.0404641628
## 4399 0.0409506872
##
## [1] "PrS_day_6_nor_PPARG_CE_up"
## $reactome
## category over_represented_pvalue
## 456 gpcr ligand binding 7.898034e-06
## 144 cell cell communication 1.457879e-05
## 517 integrin cell surface interactions 3.829954e-05
## 123 ca2 pathway 1.343681e-04
## 550 intraflagellar transport 1.838278e-04
## 40 adherens junctions interactions 2.060363e-04
## 149 cell junction organization 2.538944e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 456 0.9999966 50 229 0.009658448
## 144 0.9999947 32 127 0.009658448
## 517 0.9999893 20 69 0.016915630
## 123 0.9999632 17 56 0.044509419
## 550 0.9999530 15 49 0.045499673
## 40 0.9999471 15 47 0.045499673
## 149 0.9999059 24 97 0.048058576
##
## $go_bp
## category
## 398 cell cell adhesion via plasma membrane adhesion molecules
## 1239 heart morphogenesis
## 18 actin filament organization
## 3641 regulation of actin filament based process
## 1293 homophilic cell adhesion via plasma membrane adhesion molecules
## 38 actomyosin structure organization
## 1877 muscle tissue development
## 339 cardiac chamber morphogenesis
## 371 cartilage development
## 363 cardiac ventricle development
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 398 3.661748e-09 1.0000000 63 221
## 1239 1.239773e-08 1.0000000 57 216
## 18 6.666190e-08 1.0000000 87 420
## 3641 1.199304e-07 1.0000000 73 337
## 1293 1.533619e-07 0.9999999 45 143
## 38 1.676905e-07 0.9999999 48 187
## 1877 2.783577e-07 1.0000000 74 345
## 339 4.279965e-07 0.9999999 33 106
## 371 4.567058e-07 0.9999998 43 164
## 363 7.066016e-07 0.9999998 33 106
## FDR
## 398 1.946951e-05
## 1239 3.295937e-05
## 18 1.181471e-04
## 3641 1.486018e-04
## 1293 1.486018e-04
## 38 1.486018e-04
## 1877 2.114325e-04
## 339 2.698116e-04
## 371 2.698116e-04
## 363 3.375820e-04
##
## [1] "PrS_day_6_nor_PPARG_CE_down"
## $reactome
## category
## 1127 slc mediated transmembrane transport
## 1276 transport of bile salts and organic acids metal ions and amine compounds
## 946 response of eif2ak1 hri to heme deficiency
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1127 6.654879e-06 0.9999971 51 187
## 1276 3.187680e-05 0.9999909 22 61
## 946 7.816864e-05 0.9999920 9 15
## FDR
## 1127 0.008817715
## 1276 0.021118378
## 946 0.034524481
##
## $go_bp
## category over_represented_pvalue
## 2601 organic anion transport 5.947848e-08
## 4891 skeletal muscle organ development 1.786796e-07
## 4740 response to xenobiotic stimulus 4.540260e-07
## 3715 regulation of body fluid levels 7.387445e-07
## 3063 positive regulation of lipid catabolic process 9.376836e-07
## 5241 vascular transport 2.352882e-06
## 4056 regulation of lipid localization 2.953541e-06
## 4926 sodium ion transmembrane transport 3.421155e-06
## 3066 positive regulation of lipid metabolic process 4.116979e-06
## 1504 leukocyte proliferation 6.037574e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 2601 1.0000000 81 323 0.0003162471
## 4891 0.9999999 44 142 0.0004750196
## 4740 1.0000000 77 317 0.0008046854
## 3715 1.0000000 69 278 0.0009819761
## 3063 0.9999999 11 16 0.0009971327
## 5241 0.9999993 27 76 0.0020850453
## 4056 0.9999989 39 131 0.0022434254
## 4926 0.9999988 37 123 0.0022737849
## 3066 0.9999986 34 109 0.0024322199
## 1504 0.9999973 60 241 0.0032101783
##
## [1] "PrS_day_6_nor_PPARG_KO_up"
## $reactome
## category over_represented_pvalue
## 665 muscle contraction 9.619196e-06
## 456 gpcr ligand binding 9.879185e-05
## 123 ca2 pathway 1.104773e-04
## 517 integrin cell surface interactions 1.615082e-04
## 183 collagen chain trimerization 1.743985e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 665 0.9999966 30 157 0.01274543
## 456 0.9999565 36 229 0.04621560
## 123 0.9999738 14 56 0.04621560
## 517 0.9999572 15 68 0.04621560
## 183 0.9999659 11 38 0.04621560
##
## $go_bp
## category over_represented_pvalue
## 3179 positive regulation of osteoblast differentiation 1.557278e-09
## 869 embryonic organ development 4.500513e-09
## 870 embryonic organ morphogenesis 7.967119e-09
## 371 cartilage development 7.994094e-09
## 2642 pattern specification process 8.981302e-09
## 4896 skeletal system morphogenesis 9.153282e-09
## 2610 ossification 9.462909e-09
## 2612 osteoblast differentiation 2.995318e-08
## 4230 regulation of osteoblast differentiation 4.560799e-08
## 18 actin filament organization 8.540476e-08
## under_represented_pvalue numDEInCat numInCat FDR
## 3179 1 22 62 7.187755e-06
## 869 1 63 357 7.187755e-06
## 870 1 45 218 7.187755e-06
## 371 1 37 164 7.187755e-06
## 2642 1 59 331 7.187755e-06
## 4896 1 38 172 7.187755e-06
## 2610 1 61 350 7.187755e-06
## 2612 1 41 198 1.990763e-05
## 4230 1 28 109 2.694419e-05
## 18 1 65 417 4.540971e-05
##
## [1] "PrS_day_6_nor_PPARG_KO_down"
## $reactome
## category over_represented_pvalue
## 150 cell surface interactions at the vascular wall 3.270906e-06
## 773 peptide hormone biosynthesis 8.657772e-05
## 1127 slc mediated transmembrane transport 9.334116e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 150 0.9999991 26 95 0.00433395
## 773 0.9999957 6 9 0.04122568
## 1127 0.9999589 37 186 0.04122568
##
## $go_bp
## category over_represented_pvalue
## 3063 positive regulation of lipid catabolic process 2.541265e-08
## 3066 positive regulation of lipid metabolic process 3.765024e-08
## 4056 regulation of lipid localization 1.272134e-07
## 456 cellular ketone metabolic process 3.595200e-07
## 2601 organic anion transport 6.009201e-07
## 4923 sodium ion export across plasma membrane 7.155889e-07
## 1414 intracellular sodium ion homeostasis 1.222689e-06
## 4926 sodium ion transmembrane transport 1.539856e-06
## 3065 positive regulation of lipid localization 1.769716e-06
## 1514 lipid catabolic process 4.396169e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 3063 1.0000000 11 16 0.0001000932
## 3066 1.0000000 31 108 0.0001000932
## 4056 1.0000000 34 131 0.0002254645
## 456 0.9999999 40 174 0.0004778919
## 2601 1.0000000 60 320 0.0006341311
## 4923 1.0000000 7 8 0.0006341311
## 1414 0.9999999 9 14 0.0009287196
## 4926 0.9999995 30 120 0.0010234269
## 3065 0.9999995 24 85 0.0010455087
## 1514 0.9999981 50 261 0.0022499372
##
## [1] "PrS_day_6_nor_PPARG_PTC_up"
## $reactome
## category
## 146 cell cycle checkpoints
## 254 deposition of new cenpa containing nucleosomes at the centromere
## 943 resolution of sister chromatid cohesion
## 957 rho gtpase effectors
## 653 mitotic spindle checkpoint
## 959 rho gtpases activate formins
## 190 condensation of prophase chromosomes
## 273 diseases of programmed cell death
## 592 m phase
## 282 dna methylation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 146 8.790600e-11 1.0000000 62 282
## 254 2.288581e-10 1.0000000 25 67
## 943 6.878032e-10 1.0000000 35 118
## 957 3.394532e-09 1.0000000 61 298
## 653 4.599742e-09 1.0000000 32 110
## 959 5.187457e-09 1.0000000 36 132
## 190 1.598867e-07 1.0000000 21 66
## 273 1.798575e-07 1.0000000 27 98
## 592 2.559695e-07 1.0000000 69 398
## 282 4.533029e-07 0.9999999 19 58
## FDR
## 146 1.164755e-07
## 254 1.516185e-07
## 943 3.037797e-07
## 957 1.124439e-06
## 653 1.145563e-06
## 959 1.145563e-06
## 190 2.978891e-05
## 273 2.978891e-05
## 592 3.768440e-05
## 282 6.006264e-05
##
## $go_bp
## category over_represented_pvalue
## 4209 regulation of nuclear division 1.731047e-11
## 4132 regulation of mitotic nuclear division 1.123982e-09
## 1789 mitotic nuclear division 4.001823e-09
## 2234 negative regulation of nuclear division 4.289998e-09
## 1793 mitotic sister chromatid segregation 2.999616e-08
## 409 cell cycle checkpoint signaling 3.389289e-08
## 2592 organelle fission 3.721101e-08
## 3811 regulation of chromosome segregation 4.867973e-08
## 2005 negative regulation of cell cycle process 5.610048e-08
## 4885 sister chromatid segregation 5.876191e-08
## under_represented_pvalue numDEInCat numInCat FDR
## 4209 1 38 122 9.203976e-08
## 4132 1 32 104 2.988106e-06
## 1789 1 57 260 5.702480e-06
## 2234 1 22 58 5.702480e-06
## 1793 1 44 185 2.826442e-05
## 409 1 44 187 2.826442e-05
## 2592 1 78 426 2.826442e-05
## 3811 1 33 124 2.851121e-05
## 2005 1 57 280 2.851121e-05
## 4885 1 49 224 2.851121e-05
##
## [1] "PrS_day_6_nor_PPARG_PTC_down"
## $reactome
## category
## 1127 slc mediated transmembrane transport
## 1276 transport of bile salts and organic acids metal ions and amine compounds
## 456 gpcr ligand binding
## 172 class a 1 rhodopsin like receptors
## 629 metal ion slc transporters
## 150 cell surface interactions at the vascular wall
## 699 neutrophil degranulation
## 402 g alpha z signalling events
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1127 1.156371e-06 0.9999995 52 185
## 1276 1.365680e-06 0.9999997 24 60
## 456 1.872841e-05 0.9999911 58 230
## 172 3.268085e-05 0.9999861 41 148
## 629 1.254404e-04 0.9999798 11 23
## 150 1.402473e-04 0.9999468 28 96
## 699 1.866653e-04 0.9998893 81 388
## 402 2.065241e-04 0.9999461 16 43
## FDR
## 1127 0.0009047627
## 1276 0.0009047627
## 456 0.0082717150
## 172 0.0108255303
## 629 0.0309712885
## 150 0.0309712885
## 699 0.0342055552
## 402 0.0342055552
##
## $go_bp
## category
## 4891 skeletal muscle organ development
## 3063 positive regulation of lipid catabolic process
## 4056 regulation of lipid localization
## 51 adenylate cyclase modulating g protein coupled receptor signaling pathway
## 1874 muscle organ development
## 4926 sodium ion transmembrane transport
## 4927 sodium ion transport
## 456 cellular ketone metabolic process
## 2601 organic anion transport
## 3066 positive regulation of lipid metabolic process
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4891 4.017334e-08 1.0000000 46 142
## 3063 4.450768e-08 1.0000000 12 16
## 4056 1.613051e-07 0.9999999 42 130
## 51 8.624053e-07 0.9999997 45 150
## 1874 8.754173e-07 0.9999997 72 287
## 4926 9.139410e-07 0.9999997 38 118
## 4927 9.142938e-07 0.9999996 49 170
## 456 1.108183e-06 0.9999996 49 174
## 2601 1.406945e-06 0.9999995 78 324
## 3066 1.726383e-06 0.9999994 35 109
## FDR
## 4891 0.0001183237
## 3063 0.0001183237
## 4056 0.0002858865
## 51 0.0006944714
## 1874 0.0006944714
## 4926 0.0006944714
## 4927 0.0006944714
## 456 0.0007365260
## 2601 0.0008311917
## 3066 0.0009179178
##
## [1] "PrS_day_6_EPAS1_CE_hyp_vs_nor_up"
## $reactome
## category
## 13 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 155 cellular senescence
## 189 condensation of prophase chromosomes
## 955 rho gtpase effectors
## 707 non integrin membrane ecm interactions
## 464 hdacs deacetylate histones
## 962 rho gtpases activate pkns
## 1040 senescence associated secretory phenotype sasp
## 755 oxidative stress induced senescence
## 163 chromatin modifications during the maternal to zygotic transition mzt
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 13 8.238030e-11 1 28 58
## 155 9.220637e-11 1 58 182
## 189 1.291433e-10 1 30 66
## 955 1.321028e-10 1 80 293
## 707 2.201600e-10 1 27 53
## 464 6.268639e-10 1 35 89
## 962 6.977718e-10 1 34 85
## 1040 8.580686e-10 1 38 102
## 755 1.094995e-09 1 41 114
## 163 1.227383e-09 1 28 63
## FDR
## 13 4.369298e-08
## 155 4.369298e-08
## 189 4.369298e-08
## 955 4.369298e-08
## 707 5.825434e-08
## 464 1.318789e-07
## 962 1.318789e-07
## 1040 1.419031e-07
## 755 1.609642e-07
## 163 1.623827e-07
##
## $go_bp
## category
## 1239 heart morphogenesis
## 4161 regulation of myeloid cell differentiation
## 82 ameboidal type cell migration
## 4673 response to mechanical stimulus
## 3137 positive regulation of myeloid cell differentiation
## 4552 renal system development
## 3484 protein localization to cenp a containing chromatin
## 948 epithelial cell proliferation
## 185 astrocyte differentiation
## 2610 ossification
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1239 1.619249e-08 1.0000000 58 196
## 4161 3.779471e-08 1.0000000 47 152
## 82 1.259070e-07 1.0000000 85 355
## 4673 9.082445e-07 0.9999997 44 151
## 3137 9.984315e-07 0.9999997 26 70
## 4552 1.230168e-06 0.9999996 62 242
## 3484 2.224181e-06 0.9999998 11 18
## 948 2.756074e-06 0.9999988 74 316
## 185 3.086348e-06 0.9999992 23 60
## 2610 3.116378e-06 0.9999986 76 325
## FDR
## 1239 8.609545e-05
## 4161 1.004772e-04
## 82 2.231492e-04
## 4673 1.061732e-03
## 3137 1.061732e-03
## 4552 1.090134e-03
## 3484 1.467624e-03
## 948 1.467624e-03
## 185 1.467624e-03
## 2610 1.467624e-03
##
## [1] "PrS_day_6_EPAS1_CE_hyp_vs_nor_down"
## $reactome
## category over_represented_pvalue
## 1125 slc mediated transmembrane transport 1.818775e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1125 0.9999927 37 163 0.02406239
##
## $go_bp
## category over_represented_pvalue
## 2599 organic acid transmembrane transport 2.081206e-06
## 2601 organic anion transport 3.930837e-06
## 2472 neutral amino acid transport 6.989340e-06
## 2600 organic acid transport 2.319466e-05
## 850 electron transport chain 2.809373e-05
## 1333 import across plasma membrane 3.739141e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2599 0.9999993 30 113 0.01045013
## 2601 0.9999983 56 282 0.01045013
## 2472 0.9999986 16 44 0.01238744
## 2600 0.9999898 45 223 0.02987487
## 850 0.9999889 34 152 0.02987487
## 1333 0.9999860 30 130 0.03313502
##
## [1] "PrS_day_6_EPAS1_KO_hyp_vs_nor_up"
## $reactome
## category
## 343 extracellular matrix organization
## 184 collagen formation
## 182 collagen chain trimerization
## 181 collagen biosynthesis and modifying enzymes
## 515 integrin cell surface interactions
## 183 collagen degradation
## 56 amyloid fiber formation
## 84 assembly of collagen fibrils and other multimeric structures
## 250 degradation of the extracellular matrix
## 304 ecm proteoglycans
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 343 2.084585e-09 1.0000000 45 210
## 184 5.551136e-09 1.0000000 23 69
## 182 1.968568e-08 1.0000000 15 33
## 181 3.384177e-08 1.0000000 19 54
## 515 7.811981e-08 1.0000000 19 58
## 183 3.050528e-07 1.0000000 16 44
## 56 3.338554e-07 0.9999999 22 90
## 84 4.173698e-07 0.9999999 16 44
## 250 4.639578e-07 0.9999999 25 97
## 304 1.638737e-06 0.9999997 17 56
## FDR
## 343 2.757905e-06
## 184 3.672077e-06
## 182 8.681387e-06
## 181 1.119317e-05
## 515 2.067050e-05
## 183 6.309868e-05
## 56 6.309868e-05
## 84 6.820179e-05
## 250 6.820179e-05
## 304 2.168049e-04
##
## $go_bp
## category over_represented_pvalue
## 1239 heart morphogenesis 1.453211e-12
## 4693 response to oxygen levels 1.869788e-09
## 1877 muscle tissue development 9.244863e-09
## 2642 pattern specification process 2.628106e-08
## 1022 external encapsulating structure organization 3.822076e-08
## 645 collagen fibril organization 1.506763e-07
## 5000 striated muscle tissue development 2.173456e-07
## 948 epithelial cell proliferation 2.766740e-07
## 1875 muscle organ morphogenesis 3.016591e-07
## 353 cardiac muscle tissue morphogenesis 3.242813e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 1239 1.0000000 49 193 7.726723e-09
## 4693 1.0000000 53 270 4.970831e-06
## 1877 1.0000000 57 312 1.638498e-05
## 2642 1.0000000 52 279 3.493409e-05
## 1022 1.0000000 43 216 4.064396e-05
## 645 1.0000000 17 48 1.335243e-04
## 5000 0.9999999 38 185 1.650895e-04
## 948 1.0000000 53 312 1.724203e-04
## 1875 0.9999999 18 54 1.724203e-04
## 353 1.0000000 15 39 1.724203e-04
##
## [1] "PrS_day_6_EPAS1_KO_hyp_vs_nor_down"
## $reactome
## category
## 1202 the citric acid tca cycle and respiratory electron transport
## 943 respiratory electron transport atp synthesis by chemiosmotic coupling and heat production by uncoupling proteins
## 94 auf1 hnrnp d0 binds and destabilizes mrna
## 621 metabolism of polyamines
## 2 abc family proteins mediated transport
## 942 respiratory electron transport
## 3 abc transporter disorders
## 234 dectin 1 mediated noncanonical nf kb signaling
## 248 degradation of dvl
## 209 cross presentation of soluble exogenous antigens endosomes
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1202 7.661333e-08 1.0000000 43 171
## 943 8.596400e-08 1.0000000 35 125
## 94 9.254662e-07 0.9999998 19 52
## 621 1.774633e-06 0.9999996 19 54
## 2 2.270539e-06 0.9999994 25 86
## 942 3.143185e-06 0.9999990 28 103
## 3 4.104800e-06 0.9999990 21 67
## 234 4.565718e-06 0.9999990 19 57
## 248 6.092786e-06 0.9999987 18 53
## 209 6.974557e-06 0.9999987 16 44
## FDR
## 1202 5.686519e-05
## 943 5.686519e-05
## 94 4.081306e-04
## 621 5.869600e-04
## 2 6.007847e-04
## 942 6.930723e-04
## 3 7.550557e-04
## 234 7.550557e-04
## 248 8.956395e-04
## 209 9.227339e-04
##
## $go_bp
## category
## 2552 nucleoside triphosphate metabolic process
## 922 energy derivation by oxidation of organic compounds
## 2550 nucleoside triphosphate biosynthetic process
## 2629 oxidative phosphorylation
## 466 cellular respiration
## 850 electron transport chain
## 64 aerobic respiration
## 188 atp metabolic process
## 3555 proton transmembrane transport
## 189 atp synthesis coupled electron transport
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2552 2.295620e-11 1 46 163
## 922 3.532973e-10 1 63 285
## 2550 1.928429e-09 1 35 118
## 2629 5.003667e-09 1 37 133
## 466 6.508211e-09 1 50 217
## 850 1.118979e-08 1 39 149
## 64 2.310596e-08 1 43 177
## 188 2.365917e-08 1 34 123
## 3555 3.302985e-08 1 33 119
## 189 3.587529e-08 1 28 91
## FDR
## 2552 1.220581e-07
## 922 9.392408e-07
## 2550 3.417820e-06
## 2629 6.651124e-06
## 466 6.920831e-06
## 850 9.916015e-06
## 64 1.572447e-05
## 188 1.572447e-05
## 3555 1.907489e-05
## 189 1.907489e-05
##
## [1] "PrS_day_6_EPAS1_PTC_hyp_vs_nor_up"
## $reactome
## category
## 515 integrin cell surface interactions
## 343 extracellular matrix organization
## 304 ecm proteoglycans
## 707 non integrin membrane ecm interactions
## 250 degradation of the extracellular matrix
## 184 collagen formation
## 182 collagen chain trimerization
## 28 activation of the ap 1 family of transcription factors
## 181 collagen biosynthesis and modifying enzymes
## 606 met activates ptk2 signaling
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 515 4.862183e-07 0.9999999 21 61
## 343 5.502307e-07 0.9999998 49 221
## 304 1.609856e-06 0.9999997 20 59
## 707 2.103549e-06 0.9999996 19 55
## 250 1.345089e-05 0.9999956 27 102
## 184 2.853219e-05 0.9999919 21 73
## 182 5.203381e-05 0.9999901 13 35
## 28 8.066516e-05 0.9999961 6 9
## 181 8.138881e-05 0.9999786 17 57
## 606 9.192772e-05 0.9999846 11 28
## FDR
## 515 0.0003639776
## 343 0.0003639776
## 304 0.0006957487
## 707 0.0006957487
## 250 0.0035591067
## 184 0.0062913484
## 182 0.0098343893
## 28 0.0119641550
## 181 0.0119641550
## 606 0.0121620375
##
## $go_bp
## category over_represented_pvalue
## 5000 striated muscle tissue development 6.584172e-10
## 1239 heart morphogenesis 9.987710e-10
## 1877 muscle tissue development 1.095939e-09
## 2642 pattern specification process 7.192464e-09
## 165 appendage morphogenesis 1.343591e-08
## 164 appendage development 6.110382e-08
## 363 cardiac ventricle development 1.139033e-07
## 1874 muscle organ development 5.503470e-07
## 4896 skeletal system morphogenesis 6.600029e-07
## 659 connective tissue development 7.472347e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 5000 1.0000000 52 192 1.942369e-06
## 1239 1.0000000 53 200 1.942369e-06
## 1877 1.0000000 73 324 1.942369e-06
## 2642 1.0000000 68 304 9.560583e-06
## 165 1.0000000 34 112 1.428775e-05
## 164 1.0000000 38 141 5.414817e-05
## 363 1.0000000 31 98 8.651773e-05
## 1874 1.0000000 56 265 3.604480e-04
## 4896 0.9999998 40 164 3.604480e-04
## 659 0.9999998 49 220 3.604480e-04
##
## [1] "PrS_day_6_EPAS1_PTC_hyp_vs_nor_down"
## $reactome
## category
## 943 respiratory electron transport atp synthesis by chemiosmotic coupling and heat production by uncoupling proteins
## 1202 the citric acid tca cycle and respiratory electron transport
## 942 respiratory electron transport
## 187 complex i biogenesis
## 371 formation of atp by chemiosmotic coupling
## 94 auf1 hnrnp d0 binds and destabilizes mrna
## 151 cellular response to chemical stress
## 2 abc family proteins mediated transport
## 643 mitochondrial translation
## 207 cristae formation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 943 8.068830e-16 1.0000000 56 125
## 1202 8.890067e-14 1.0000000 64 171
## 942 6.550290e-12 1.0000000 44 103
## 187 7.197179e-07 0.9999998 24 57
## 371 1.152116e-06 0.9999999 12 18
## 94 6.231576e-06 0.9999985 21 52
## 151 7.216446e-06 0.9999968 51 194
## 2 7.478901e-06 0.9999976 30 92
## 643 9.913609e-06 0.9999967 31 94
## 207 1.018834e-05 0.9999983 15 31
## FDR
## 943 1.067506e-12
## 1202 5.880779e-11
## 942 2.888678e-09
## 187 2.380467e-04
## 371 3.048500e-04
## 94 1.236823e-03
## 151 1.236823e-03
## 2 1.236823e-03
## 643 1.347917e-03
## 207 1.347917e-03
##
## $go_bp
## category
## 2629 oxidative phosphorylation
## 850 electron transport chain
## 64 aerobic respiration
## 466 cellular respiration
## 189 atp synthesis coupled electron transport
## 4571 respiratory electron transport chain
## 922 energy derivation by oxidation of organic compounds
## 2552 nucleoside triphosphate metabolic process
## 3554 proton motive force driven atp synthesis
## 2550 nucleoside triphosphate biosynthetic process
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2629 4.584301e-18 1 59 133
## 850 3.869701e-16 1 61 153
## 64 1.685665e-15 1 66 178
## 466 1.968407e-15 1 75 219
## 189 1.992795e-15 1 44 91
## 4571 2.686586e-14 1 48 112
## 922 1.967939e-13 1 85 289
## 2552 4.729783e-12 1 57 167
## 3554 4.837058e-12 1 35 74
## 2550 2.013260e-11 1 45 118
## FDR
## 2629 2.437473e-14
## 850 1.028760e-12
## 64 2.119138e-12
## 466 2.119138e-12
## 189 2.119138e-12
## 4571 2.380763e-11
## 922 1.494791e-10
## 2552 2.857626e-09
## 3554 2.857626e-09
## 2550 1.070450e-08
##
## [1] "PrS_day_6_WT_WT_hyp_vs_nor_up"
## $reactome
## category
## 466 hdacs deacetylate histones
## 56 amyloid fiber formation
## 606 meiotic recombination
## 282 dna methylation
## 86 assembly of the orc complex at the origin of replication
## 13 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 254 deposition of new cenpa containing nucleosomes at the centromere
## 1125 sirt1 negatively regulates rrna expression
## 190 condensation of prophase chromosomes
## 757 oxidative stress induced senescence
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 466 1.839398e-12 1 40 90
## 56 9.165630e-12 1 40 94
## 606 8.444486e-11 1 35 79
## 282 1.262692e-10 1 29 59
## 86 1.407572e-10 1 30 63
## 13 1.584806e-10 1 29 60
## 254 2.570763e-10 1 31 68
## 1125 4.278800e-10 1 29 62
## 190 7.900714e-10 1 30 67
## 757 1.034177e-09 1 44 117
## FDR
## 466 2.437203e-09
## 56 6.072230e-09
## 606 3.499781e-08
## 282 3.499781e-08
## 86 3.499781e-08
## 13 3.499781e-08
## 254 4.866086e-08
## 1125 7.086763e-08
## 190 1.163161e-07
## 757 1.370285e-07
##
## $go_bp
## category
## 2642 pattern specification process
## 1293 homophilic cell adhesion via plasma membrane adhesion molecules
## 398 cell cell adhesion via plasma membrane adhesion molecules
## 1239 heart morphogenesis
## 164 appendage development
## 165 appendage morphogenesis
## 5000 striated muscle tissue development
## 214 axon guidance
## 1022 external encapsulating structure organization
## 1877 muscle tissue development
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2642 1.964648e-12 1.0000000 109 338
## 1293 3.272453e-12 1.0000000 62 137
## 398 2.139354e-11 1.0000000 81 215
## 1239 4.214341e-09 1.0000000 72 217
## 164 1.404575e-08 1.0000000 52 146
## 165 2.424452e-08 1.0000000 44 116
## 5000 3.850266e-08 1.0000000 67 209
## 214 1.272362e-07 0.9999999 60 182
## 1022 2.726303e-07 1.0000000 76 260
## 1877 2.893302e-07 1.0000000 95 348
## FDR
## 2642 8.699815e-09
## 1293 8.699815e-09
## 398 3.791649e-08
## 1239 5.601913e-06
## 164 1.493625e-05
## 165 2.148468e-05
## 5000 2.924552e-05
## 214 8.456437e-05
## 1022 1.538369e-04
## 1877 1.538369e-04
##
## [1] "PrS_day_6_WT_WT_hyp_vs_nor_down"
## $reactome
## category
## 152 cellular response to chemical stress
## 730 nuclear events mediated by nfe2l2
## 568 keap1 nfe2l2 pathway
## 623 metabolism of polyamines
## 94 auf1 hnrnp d0 binds and destabilizes mrna
## 945 respiratory electron transport atp synthesis by chemiosmotic coupling and heat production by uncoupling proteins
## 210 cross presentation of soluble exogenous antigens endosomes
## 1204 the citric acid tca cycle and respiratory electron transport
## 250 degradation of dvl
## 944 respiratory electron transport
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 152 4.182472e-09 1.0000000 83 197
## 730 5.610407e-09 1.0000000 48 94
## 568 9.025730e-09 1.0000000 57 121
## 623 1.767221e-08 1.0000000 33 56
## 94 3.459032e-08 1.0000000 31 52
## 945 3.976105e-08 1.0000000 58 126
## 210 1.080434e-07 1.0000000 27 44
## 1204 1.279762e-07 0.9999999 72 173
## 250 2.935247e-07 0.9999999 30 53
## 944 3.594945e-07 0.9999999 48 103
## FDR
## 152 3.716895e-06
## 730 3.716895e-06
## 568 3.986364e-06
## 623 5.853920e-06
## 94 8.780565e-06
## 945 8.780565e-06
## 210 2.045106e-05
## 1204 2.119607e-05
## 250 4.321336e-05
## 944 4.763301e-05
##
## $go_bp
## category
## 3555 proton transmembrane transport
## 922 energy derivation by oxidation of organic compounds
## 4783 ribosome biogenesis
## 2629 oxidative phosphorylation
## 4612 response to endoplasmic reticulum stress
## 850 electron transport chain
## 189 atp synthesis coupled electron transport
## 466 cellular respiration
## 4571 respiratory electron transport chain
## 64 aerobic respiration
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3555 1.781999e-10 1 61 129
## 922 4.902791e-10 1 111 298
## 4783 1.191437e-09 1 115 315
## 2629 9.222683e-09 1 60 136
## 4612 1.047022e-08 1 91 244
## 850 1.518248e-08 1 66 157
## 189 2.325707e-08 1 45 93
## 466 4.964408e-08 1 84 224
## 4571 6.267356e-08 1 51 114
## 64 9.493106e-08 1 72 183
## FDR
## 3555 9.474888e-07
## 922 1.303407e-06
## 4783 2.111624e-06
## 2629 1.113403e-05
## 4612 1.113403e-05
## 850 1.345421e-05
## 189 1.766541e-05
## 466 3.299470e-05
## 4571 3.702615e-05
## 64 5.047484e-05enrichment_output_dir = file.path(result_dir, "enrichment")
if (!file.exists(enrichment_output_dir)){
dir.create(enrichment_output_dir, recursive = TRUE)
}
saveRDS(goseq_res,
file.path(enrichment_output_dir,
sprintf("%s_enrichment.rds", release_name))) gc()## used (Mb) gc trigger (Mb) max used (Mb)
## Ncells 8884314 474.5 16044431 856.9 16044431 856.9
## Vcells 20446264 156.0 73524670 561.0 73524670 561.0sessionInfo()## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.6 LTS
##
## Matrix products: default
## BLAS/LAPACK: /app/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib/libflexiblas.so.3.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.14.0
## [2] GenomicFeatures_1.46.1
## [3] GenomicRanges_1.46.1
## [4] GenomeInfoDb_1.30.1
## [5] org.Hs.eg.db_3.14.0
## [6] AnnotationDbi_1.56.2
## [7] IRanges_2.28.0
## [8] S4Vectors_0.32.4
## [9] Biobase_2.54.0
## [10] BiocGenerics_0.40.0
## [11] data.table_1.14.2
## [12] dplyr_1.0.7
## [13] fgsea_1.20.0
## [14] goseq_1.46.0
## [15] geneLenDataBase_1.30.0
## [16] BiasedUrn_1.07
## [17] RColorBrewer_1.1-2
## [18] stringr_1.4.0
## [19] ggpubr_0.4.0
## [20] ggrepel_0.9.1
## [21] ggplot2_3.5.1
## [22] rmarkdown_2.11
##
## loaded via a namespace (and not attached):
## [1] colorspace_2.0-2 ggsignif_0.6.3
## [3] rjson_0.2.20 ellipsis_0.3.2
## [5] rio_0.5.27 XVector_0.34.0
## [7] bit64_4.0.5 fansi_0.5.0
## [9] xml2_1.3.2 splines_4.1.2
## [11] cachem_1.0.6 knitr_1.36
## [13] jsonlite_1.7.2 Cairo_1.5-12.2
## [15] Rsamtools_2.10.0 broom_0.7.10
## [17] GO.db_3.14.0 dbplyr_2.1.1
## [19] png_0.1-7 compiler_4.1.2
## [21] httr_1.4.2 backports_1.3.0
## [23] assertthat_0.2.1 Matrix_1.6-4
## [25] fastmap_1.1.0 cli_3.6.3
## [27] htmltools_0.5.2 prettyunits_1.1.1
## [29] tools_4.1.2 gtable_0.3.0
## [31] glue_1.4.2 GenomeInfoDbData_1.2.7
## [33] rappdirs_0.3.3 fastmatch_1.1-3
## [35] Rcpp_1.0.7 carData_3.0-4
## [37] cellranger_1.1.0 jquerylib_0.1.4
## [39] vctrs_0.6.5 Biostrings_2.62.0
## [41] nlme_3.1-153 rtracklayer_1.54.0
## [43] xfun_0.27 openxlsx_4.2.4
## [45] lifecycle_1.0.4 restfulr_0.0.13
## [47] rstatix_0.7.0 XML_3.99-0.8
## [49] zlibbioc_1.40.0 scales_1.3.0
## [51] hms_1.1.1 MatrixGenerics_1.6.0
## [53] parallel_4.1.2 SummarizedExperiment_1.24.0
## [55] yaml_2.2.1 curl_4.3.2
## [57] gridExtra_2.3 memoise_2.0.0
## [59] sass_0.4.0 biomaRt_2.50.3
## [61] stringi_1.7.5 RSQLite_2.2.8
## [63] highr_0.9 BiocIO_1.4.0
## [65] filelock_1.0.3 zip_2.2.0
## [67] BiocParallel_1.28.3 rlang_1.1.4
## [69] pkgconfig_2.0.3 matrixStats_1.3.0
## [71] bitops_1.0-7 evaluate_0.14
## [73] lattice_0.20-45 purrr_0.3.4
## [75] GenomicAlignments_1.30.0 bit_4.0.4
## [77] tidyselect_1.1.1 magrittr_2.0.1
## [79] R6_2.5.1 generics_0.1.3
## [81] DelayedArray_0.20.0 DBI_1.1.1
## [83] mgcv_1.8-38 pillar_1.6.4
## [85] haven_2.4.3 foreign_0.8-81
## [87] withr_3.0.0 KEGGREST_1.34.0
## [89] abind_1.4-5 RCurl_1.98-1.5
## [91] tibble_3.1.5 crayon_1.4.2
## [93] car_3.0-11 utf8_1.2.2
## [95] BiocFileCache_2.2.1 progress_1.2.2
## [97] grid_4.1.2 readxl_1.3.1
## [99] blob_1.2.2 forcats_0.5.1
## [101] digest_0.6.28 tidyr_1.1.4
## [103] munsell_0.5.0 bslib_0.3.1